Bay Area Biotech Industry Braces for Gene Patenting Court Case
Turkey Trouble: Genetics Gone Too Far?
Genome 3.0: ENCODE Takes Our DNA From Junk to Treasure
The Results Are In For My Genetics Quiz
The Heat is On For California Wines
Arm Yourselves for the Upcoming (Genetics) Revolution
Building a Better, Tastier Tomato
Pregnant Women Face Big Questions With Cheaper DNA Sequencing
Tackling the Cause of Cystic Fibrosis One Mutation at a Time
Sponsored
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Together these two partners created the \u003ca href=\"http://www.thetech.org/exhibits/permanent/index.php?sGalKey=gtwt&galKey=lt\">Genetics: Technology with a Twist\u003c/a> exhibition.\r\n\r\nYou can also see \u003ca href=\"https://ww2.kqed.org/science/author/dr-barry-starr/\">additional posts by Barry at KQED Science\u003c/a>, and read his \u003ca href=\"http://science.kqed.org/quest/author/dr-barry-starr/\">previous contributions\u003c/a> to \u003ca href=\"http://science.kqed.org/quest/\">QUEST\u003c/a>, a project dedicated to exploring the Science of Sustainability.","avatar":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g","twitter":"geneticsboy","facebook":null,"instagram":null,"linkedin":null,"sites":[{"site":"science","roles":["author"]},{"site":"quest","roles":["subscriber"]}],"headData":{"title":"Dr. Barry Starr | KQED","description":null,"ogImgSrc":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g","twImgSrc":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g"},"isLoading":false,"link":"/author/dr-barry-starr"}},"breakingNewsReducer":{},"campaignFinanceReducer":{},"firebase":{"requesting":{},"requested":{},"timestamps":{},"data":{},"ordered":{},"auth":{"isLoaded":false,"isEmpty":true},"authError":null,"profile":{"isLoaded":false,"isEmpty":true},"listeners":{"byId":{},"allIds":[]},"isInitializing":false,"errors":[]},"navBarReducer":{"navBarId":"home","fullView":true,"showPlayer":false},"navMenuReducer":{"menus":[{"key":"menu1","items":[{"name":"News","link":"/","type":"title"},{"name":"Politics","link":"/politics"},{"name":"Science","link":"/science"},{"name":"Education","link":"/educationnews"},{"name":"Housing","link":"/housing"},{"name":"Immigration","link":"/immigration"},{"name":"Criminal Justice","link":"/criminaljustice"},{"name":"Silicon Valley","link":"/siliconvalley"},{"name":"Forum","link":"/forum"},{"name":"The California Report","link":"/californiareport"}]},{"key":"menu2","items":[{"name":"Arts & Culture","link":"/arts","type":"title"},{"name":"Critics’ Picks","link":"/thedolist"},{"name":"Cultural Commentary","link":"/artscommentary"},{"name":"Food & Drink","link":"/food"},{"name":"Bay Area Hip-Hop","link":"/bayareahiphop"},{"name":"Rebel Girls","link":"/rebelgirls"},{"name":"Arts Video","link":"/artsvideos"}]},{"key":"menu3","items":[{"name":"Podcasts","link":"/podcasts","type":"title"},{"name":"Bay Curious","link":"/podcasts/baycurious"},{"name":"Rightnowish","link":"/podcasts/rightnowish"},{"name":"The Bay","link":"/podcasts/thebay"},{"name":"On Our Watch","link":"/podcasts/onourwatch"},{"name":"Mindshift","link":"/podcasts/mindshift"},{"name":"Consider This","link":"/podcasts/considerthis"},{"name":"Political Breakdown","link":"/podcasts/politicalbreakdown"}]},{"key":"menu4","items":[{"name":"Live Radio","link":"/radio","type":"title"},{"name":"TV","link":"/tv","type":"title"},{"name":"Events","link":"/events","type":"title"},{"name":"For Educators","link":"/education","type":"title"},{"name":"Support KQED","link":"/support","type":"title"},{"name":"About","link":"/about","type":"title"},{"name":"Help Center","link":"https://kqed-helpcenter.kqed.org/s","type":"title"}]}]},"pagesReducer":{},"postsReducer":{"stream_live":{"type":"live","id":"stream_live","audioUrl":"https://streams.kqed.org/kqedradio","title":"Live Stream","excerpt":"Live Stream information currently unavailable.","link":"/radio","featImg":"","label":{"name":"KQED Live","link":"/"}},"stream_kqedNewscast":{"type":"posts","id":"stream_kqedNewscast","audioUrl":"https://www.kqed.org/.stream/anon/radio/RDnews/newscast.mp3?_=1","title":"KQED Newscast","featImg":"","label":{"name":"88.5 FM","link":"/"}},"quest_52297":{"type":"posts","id":"quest_52297","meta":{"index":"posts_1591205157","site":"quest","id":"52297","score":null,"sort":[1365802017000]},"guestAuthors":[],"slug":"bay-area-biotech-industry-braces-for-gene-patenting-court-case","title":"Bay Area Biotech Industry Braces for Gene Patenting Court Case","publishDate":1365802017,"format":"audio","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cp>http://www.kqed.org/.stream/anon/radio/quest/2013/04/20130415science.mp3\u003c/p>\n\u003cp>Bay Area biotechnology companies are keeping an eye on the nation’s highest court. On Monday, the Supreme Court will hear a case on a key question: can you patent a human gene?\u003c/p>\n\u003cp>A recent study estimates that close to half of human genes identified so far are already patented. The court’s ruling could put millions of dollars at stake for Bay Area universities and biotech companies. \u003c/p>\n\u003cp>At issue are two genes related to breast and ovarian cancer, \u003ca href=\"http://blogs.kqed.org/stateofhealth/2013/04/12/breast-cancer-gene-mutations-at-heart-of-supreme-court-case/#more-12082\">BRCA 1 and BRCA 2\u003c/a>. Women with mutations in these genes are five to eight times more likely to develop breast cancer. To gauge that risk, patients often get a genetic test. It’s one of the most common tests that genetic counselors handle, like Julie Mak at\u003ca href=\"http://cancer.ucsf.edu/\"> UCSF’s Cancer Center\u003c/a>in San Francisco.\u003c/p>\n\u003cfigure id=\"attachment_52321\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/sequencing.jpg\">\u003cimg class=\"size-thumbnail wp-image-52321 \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/sequencing-300x169.jpg\" alt=\"Preparation for DNA sequencing (Maggie Bartlett, NHGRI)\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Preparation for DNA sequencing (Maggie Bartlett, NHGRI)\u003c/figcaption>\u003c/figure>\n\u003cp>“I do think it opens up a very loaded set of questions for people who are sometimes very young,” says Mak. “As you can imagine, the things we talk about with people are very serious and sometimes stressful and upsetting.”\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>A blood or saliva sample can tell a woman if she has those mutations, but that test isn’t run at UCSF. “For most BRCA 1 and 2 testing, the lab in Utah is the only one that does this testing,” Mak says, referring to Myriad Genetics.\u003c/p>\n\u003cp>\u003ca href=\"http://www.myriad.com/\">Myriad Genetics\u003c/a> holds patents on not only the test, but the actual genes themselves. That means one company has a monopoly on those genes and theoretically controls what can be done with them. That’s what’s being challenged by the American Civil Liberties Union.\u003c/p>\n\u003cp>\u003cstrong>Natural or Not?\u003c/strong>\u003c/p>\n\u003cp>“A lot of people wonder: how can you patent a gene?” says Mildred Cho, associate director of the \u003ca href=\"http://bioethics.stanford.edu/\">Stanford Center for Biomedical Ethics\u003c/a>.\u003c/p>\n\u003cp>In the case, the ACLU is arguing that genes aren’t patentable because they’re naturally occurring -- they’re found inside our bodies. According to patent law, “products of nature are not patentable,” Cho says.\u003c/p>\n\u003cp>Myriad Genetics argues that by extracting a specific gene and isolating it, it turns into a man-made invention, which makes it patentable. “In order to analyze to DNA, you have to break open the cells and break the DNA up in to little pieces,” Cho explains.\u003c/p>\n\u003cp>Legal complexities aside, Cho says it has real effects on our healthcare decision, like getting a second opinion. “No laboratory has 100 percent accuracy and so you would ideally want to have a lab result that’s really important confirmed by another lab,” she says. “You can’t do that if there are patents on that lab test.”\u003c/p>\n\u003cp>\u003cstrong>Questions of Open Access\u003c/strong>\u003c/p>\n\u003cp>Patents can also affect genetic research, according to UCSF professor Dr. Robert Nusssbaum. When I meet him in his office, he’s wearing a button pinned to his shirt.\u003c/p>\n\u003cp>“So my button says ‘free the data,'” he points out.\u003c/p>\n\u003cp>Since DNA doesn’t come with an instruction manual that reveals if a genetic mutation is harmful or not, the only way to find out is to compare it to thousands of other genetic tests.\u003c/p>\n\u003cp>“The only way to make that happen faster is for all the laboratories to pool all their information in one place and all have access to it,” Nussbaum says.\u003c/p>\n\u003cp>But not everyone is sharing. “There are a couple of laboratories, and Myriad is one of them, that have decided that since they had the patent on testing, that they would keep their data locked up as intellectual property,” he says.\u003c/p>\n\u003cp>In response, Nussbaum has organized an \u003ca href=\"http://www.sharingclinicalreports.org/\">open source database\u003c/a> that holds genetic data about breast cancer mutations, free for researchers to use.\u003c/p>\n\u003cp>“In terms of gene testing, I think patents are of no value, period,” says Nussbaum.\u003c/p>\n\u003cp>\u003cstrong>Basis of Biotech\u003c/strong>\u003c/p>\n\u003cp>“Patents are a very important, fundamental part of the foundation on which the biotechnology, biopharmaceutical industry has been built,” says Sean Johnston, general counsel at \u003ca href=\"http://www.gene.com/\">Genentech\u003c/a> in South San Francisco, one of the largest biotech companies in the world.\u003c/p>\n\u003cp>Companies like Genentech use genetic information to develop drugs and treatments, in addition to genetic diagnostic tests.\u003c/p>\n\u003cp>“Biotech and biopharmaceutical companies have relied upon patent protection to justify the significant investment, the risk-taking and the innovation that is necessary to develop new drugs,” Johnston says.\u003c/p>\n\u003cp>Johnston says it often takes a billion dollars to bring a drug to market, an investment that could be tougher to make without the protection of gene patents.\u003c/p>\n\u003cp>“It’s not a matter that if the court were to rule broadly our business would be destroyed,” Johnston says. “But in theory I think it has the potential to be very disruptive to the industry.”\u003c/p>\n\u003cp>\u003cstrong>Universities in the Middle\u003c/strong>\u003c/p>\n\u003cp>Biotech companies here aren’t the only ones watching this case. The University of California as a whole is one of the top ten gene patent holders in the country.\u003c/p>\n\u003cp>“Universities are often accused of patenting solely for the purpose of getting financial gain,” says Karin Immergluck of UCSF’s Office of Technology Management. The office handles several hundred gene patents.\u003c/p>\n\u003cp>“UCSF’s first goal is to translate our really exciting, cutting-edge technologies into products and services that will benefit the public,” she says.\u003c/p>\n\u003cp>The university walks a fine line. Companies pay millions of dollars a year to use its patents, like the one related to human growth hormone. But the court case brings up issue in licensing patents that universities already grappling with.\u003c/p>\n\u003cp>“For example, making sure the rights aren’t completely locked up in one company so that underinsured patients don’t have access,” says Immergluck.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Patient access, biotech industry profits and innovation could all be affected by the Supreme Court’s ruling. It’s expected in June.\u003c/p>\n\n","blocks":[],"excerpt":"The Supreme Court is hearing a case on a key question: can you patent a human gene? ","status":"publish","parent":0,"modified":1366389328,"stats":{"hasAudio":true,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":34,"wordCount":1025},"headData":{"title":"Bay Area Biotech Industry Braces for Gene Patenting Court Case | KQED","description":"The Supreme Court is hearing a case on a key question: can you patent a human gene? ","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"52297 http://science.kqed.org/quest/?post_type=audio_reports&p=52297","disqusUrl":"https://ww2.kqed.org/quest/2013/04/12/bay-area-biotech-industry-braces-for-gene-patenting-court-case/","disqusTitle":"Bay Area Biotech Industry Braces for Gene Patenting Court Case","WpOldSlug":"west-coast-a-test-bed-for-ocean-acidification-2","path":"/quest/52297/bay-area-biotech-industry-braces-for-gene-patenting-court-case","audioUrl":"http://www.kqed.org/.stream/anon/radio/quest/2013/04/20130415science.mp3","audioDuration":null,"audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"audioLink","attributes":{"named":{"src":"http://www.kqed.org/.stream/anon/radio/quest/2013/04/20130415science.mp3"},"numeric":[]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>Bay Area biotechnology companies are keeping an eye on the nation’s highest court. On Monday, the Supreme Court will hear a case on a key question: can you patent a human gene?\u003c/p>\n\u003cp>A recent study estimates that close to half of human genes identified so far are already patented. The court’s ruling could put millions of dollars at stake for Bay Area universities and biotech companies. \u003c/p>\n\u003cp>At issue are two genes related to breast and ovarian cancer, \u003ca href=\"http://blogs.kqed.org/stateofhealth/2013/04/12/breast-cancer-gene-mutations-at-heart-of-supreme-court-case/#more-12082\">BRCA 1 and BRCA 2\u003c/a>. Women with mutations in these genes are five to eight times more likely to develop breast cancer. To gauge that risk, patients often get a genetic test. It’s one of the most common tests that genetic counselors handle, like Julie Mak at\u003ca href=\"http://cancer.ucsf.edu/\"> UCSF’s Cancer Center\u003c/a>in San Francisco.\u003c/p>\n\u003cfigure id=\"attachment_52321\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/sequencing.jpg\">\u003cimg class=\"size-thumbnail wp-image-52321 \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/sequencing-300x169.jpg\" alt=\"Preparation for DNA sequencing (Maggie Bartlett, NHGRI)\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Preparation for DNA sequencing (Maggie Bartlett, NHGRI)\u003c/figcaption>\u003c/figure>\n\u003cp>“I do think it opens up a very loaded set of questions for people who are sometimes very young,” says Mak. “As you can imagine, the things we talk about with people are very serious and sometimes stressful and upsetting.”\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>A blood or saliva sample can tell a woman if she has those mutations, but that test isn’t run at UCSF. “For most BRCA 1 and 2 testing, the lab in Utah is the only one that does this testing,” Mak says, referring to Myriad Genetics.\u003c/p>\n\u003cp>\u003ca href=\"http://www.myriad.com/\">Myriad Genetics\u003c/a> holds patents on not only the test, but the actual genes themselves. That means one company has a monopoly on those genes and theoretically controls what can be done with them. That’s what’s being challenged by the American Civil Liberties Union.\u003c/p>\n\u003cp>\u003cstrong>Natural or Not?\u003c/strong>\u003c/p>\n\u003cp>“A lot of people wonder: how can you patent a gene?” says Mildred Cho, associate director of the \u003ca href=\"http://bioethics.stanford.edu/\">Stanford Center for Biomedical Ethics\u003c/a>.\u003c/p>\n\u003cp>In the case, the ACLU is arguing that genes aren’t patentable because they’re naturally occurring -- they’re found inside our bodies. According to patent law, “products of nature are not patentable,” Cho says.\u003c/p>\n\u003cp>Myriad Genetics argues that by extracting a specific gene and isolating it, it turns into a man-made invention, which makes it patentable. “In order to analyze to DNA, you have to break open the cells and break the DNA up in to little pieces,” Cho explains.\u003c/p>\n\u003cp>Legal complexities aside, Cho says it has real effects on our healthcare decision, like getting a second opinion. “No laboratory has 100 percent accuracy and so you would ideally want to have a lab result that’s really important confirmed by another lab,” she says. “You can’t do that if there are patents on that lab test.”\u003c/p>\n\u003cp>\u003cstrong>Questions of Open Access\u003c/strong>\u003c/p>\n\u003cp>Patents can also affect genetic research, according to UCSF professor Dr. Robert Nusssbaum. When I meet him in his office, he’s wearing a button pinned to his shirt.\u003c/p>\n\u003cp>“So my button says ‘free the data,'” he points out.\u003c/p>\n\u003cp>Since DNA doesn’t come with an instruction manual that reveals if a genetic mutation is harmful or not, the only way to find out is to compare it to thousands of other genetic tests.\u003c/p>\n\u003cp>“The only way to make that happen faster is for all the laboratories to pool all their information in one place and all have access to it,” Nussbaum says.\u003c/p>\n\u003cp>But not everyone is sharing. “There are a couple of laboratories, and Myriad is one of them, that have decided that since they had the patent on testing, that they would keep their data locked up as intellectual property,” he says.\u003c/p>\n\u003cp>In response, Nussbaum has organized an \u003ca href=\"http://www.sharingclinicalreports.org/\">open source database\u003c/a> that holds genetic data about breast cancer mutations, free for researchers to use.\u003c/p>\n\u003cp>“In terms of gene testing, I think patents are of no value, period,” says Nussbaum.\u003c/p>\n\u003cp>\u003cstrong>Basis of Biotech\u003c/strong>\u003c/p>\n\u003cp>“Patents are a very important, fundamental part of the foundation on which the biotechnology, biopharmaceutical industry has been built,” says Sean Johnston, general counsel at \u003ca href=\"http://www.gene.com/\">Genentech\u003c/a> in South San Francisco, one of the largest biotech companies in the world.\u003c/p>\n\u003cp>Companies like Genentech use genetic information to develop drugs and treatments, in addition to genetic diagnostic tests.\u003c/p>\n\u003cp>“Biotech and biopharmaceutical companies have relied upon patent protection to justify the significant investment, the risk-taking and the innovation that is necessary to develop new drugs,” Johnston says.\u003c/p>\n\u003cp>Johnston says it often takes a billion dollars to bring a drug to market, an investment that could be tougher to make without the protection of gene patents.\u003c/p>\n\u003cp>“It’s not a matter that if the court were to rule broadly our business would be destroyed,” Johnston says. “But in theory I think it has the potential to be very disruptive to the industry.”\u003c/p>\n\u003cp>\u003cstrong>Universities in the Middle\u003c/strong>\u003c/p>\n\u003cp>Biotech companies here aren’t the only ones watching this case. The University of California as a whole is one of the top ten gene patent holders in the country.\u003c/p>\n\u003cp>“Universities are often accused of patenting solely for the purpose of getting financial gain,” says Karin Immergluck of UCSF’s Office of Technology Management. The office handles several hundred gene patents.\u003c/p>\n\u003cp>“UCSF’s first goal is to translate our really exciting, cutting-edge technologies into products and services that will benefit the public,” she says.\u003c/p>\n\u003cp>The university walks a fine line. Companies pay millions of dollars a year to use its patents, like the one related to human growth hormone. But the court case brings up issue in licensing patents that universities already grappling with.\u003c/p>\n\u003cp>“For example, making sure the rights aren’t completely locked up in one company so that underinsured patients don’t have access,” says Immergluck.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Patient access, biotech industry profits and innovation could all be affected by the Supreme Court’s ruling. It’s expected in June.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/52297/bay-area-biotech-industry-braces-for-gene-patenting-court-case","authors":["239"],"categories":["quest_5","quest_12"],"tags":["quest_252","quest_9951","quest_475","quest_13194","quest_848","quest_11907","quest_1192","quest_1197","quest_13201","quest_11518","quest_13203","quest_11908","quest_2841"],"featImg":"quest_52321","label":"quest"},"quest_47023":{"type":"posts","id":"quest_47023","meta":{"index":"posts_1591205157","site":"quest","id":"47023","score":null,"sort":[1353340828000]},"guestAuthors":[],"slug":"turkey-trouble-genetics-gone-too-far","title":"Turkey Trouble: Genetics Gone Too Far?","publishDate":1353340828,"format":"aside","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_47026\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/11/19/turkey-trouble-genetics-gone-too-far/turkeyfarm/\" rel=\"attachment wp-att-47026\">\u003cimg class=\"size-full wp-image-47026\" title=\"TurkeyFarm\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/11/TurkeyFarm.jpg\" alt=\"\" width=\"640\" height=\"356\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/11/TurkeyFarm.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/11/TurkeyFarm-400x223.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We've bred these poor things to the point where they can't even reproduce anymore without our help.\u003c/figcaption>\u003c/figure>\n\u003cp>No, this isn’t a blog about genetically modified organisms -- that has been argued enough lately! Instead, in honor of Thanksgiving, I want to talk about regular old selective breeding and the monsters it can create: the industrial turkey, the main course at most dinner tables on Thursday.\u003c/p>\n\u003cp>What we have all conspired to do to this once noble bird is appallingly awful. In our drive for more healthy white meat, we have selected for giant versions of turkeys with grotesquely over-sized breasts. How over-sized? Their breasts are so big at this point that these poor things can’t successfully mate. Every industrial turkey was created by artificial insemination.\u003c/p>\n\u003cp>Not only that, but all of that extra muscle has created birds in constant pain. Their bones just can’t easily handle all of that muscle being packed on so quickly. Add the damage to their hearts and the resulting high rate of heart attacks and you have something pretty close to monstrous.\u003c/p>\n\u003cp>And remember, we didn’t engineer these things at all. These caricatures of wild turkeys were hidden in the turkey genome all along.\u003c/p>\n\u003cp>Most species have an incredible amount of variation prepacked into their genomes. Look at a Great Dane and a Chihuahua and you’ll know what I mean! Both came from the same basic set of recipes, the wolf genome.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Wild turkeys have a wide range of possible turkeys hidden in their genome too. The current industrial turkey is just a certain combination of all of the different gene versions (or alleles) that were already present.\u003c/p>\n\u003cfigure id=\"attachment_47031\" class=\"wp-caption alignright\" style=\"max-width: 170px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/11/19/turkey-trouble-genetics-gone-too-far/goldenretriever/\" rel=\"attachment wp-att-47031\">\u003cimg class=\"size-full wp-image-47031\" title=\"GoldenRetriever\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/11/GoldenRetriever.jpg\" alt=\"\" width=\"170\" height=\"267\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">It doesn't just stop at turkeys either. Breeding for specific traits affects other animals too.\u003c/figcaption>\u003c/figure>\n\u003cp>Of course, if nature had stumbled on this particular combination of alleles in the wild, the resulting turkey would not have survived. Even if it managed to avoid bone damage and heart attacks, the thing couldn't successfully breed anyway. No, this turkey would have mercifully died out.\u003c/p>\n\u003cp>The situation is different on the factory farm. There the traits which would have doomed this turkey are selected for and this turkey ends up the “winner.” There are definitely different pressures in natural and artificial selection!\u003c/p>\n\u003cp>All of this raises the obvious ethical question. Just because we can breed this turkey, should we? The turkey lives a short, miserable life but we get an affordable, healthy source of protein. It is obvious which choice we’ve made as a society, but is it the right one?\u003c/p>\n\u003cp>And of course this discussion shouldn’t stop at the turkey. Chickens are having heart attacks all over the place, golden retrievers have a \u003ca href=\"http://genetics.thetech.org/ask/ask449\">ridiculously high rate of cancer\u003c/a>, and so on for many other artificially selected animals. Should we let this continue so we can have cheaper meat or a dog that looks just so?\u003c/p>\n\u003cp>Before ending, I do want to say that I am not opposed to all artificial selection. Without it, we’d have very few of the crops we have now. Our corn wouldn’t be as sweet, our grapes and bananas would have seeds and so on. It is just that we might want to be more careful in what we create. Especially when we tinker with animals.\u003c/p>\n\u003cp>\u003cstrong>Additional Reading:\u003c/strong>\u003c/p>\n\u003cp>\u003ca href=\"http://www.wired.com/wiredscience/2008/11/turkeytech/\">Great Wired Science Article on the Topic\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://ps.fass.org/content/77/12/1773.long\">Article on problems associated with rapid growth\u003c/a>\u003c/p>\n\n","blocks":[],"excerpt":"No, this isn’t a blog about genetically modified organisms -- that has been argued enough lately! Instead, in honor of Thanksgiving, I want to talk about regular old selective breeding and the monsters it can create.","status":"publish","parent":0,"modified":1366756621,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":16,"wordCount":584},"headData":{"title":"Turkey Trouble: Genetics Gone Too Far? | KQED","description":"No, this isn’t a blog about genetically modified organisms -- that has been argued enough lately! Instead, in honor of Thanksgiving, I want to talk about regular old selective breeding and the monsters it can create.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"47023 http://science.kqed.org/quest/?p=47023","disqusUrl":"https://ww2.kqed.org/quest/2012/11/19/turkey-trouble-genetics-gone-too-far/","disqusTitle":"Turkey Trouble: Genetics Gone Too Far?","path":"/quest/47023/turkey-trouble-genetics-gone-too-far","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_47026\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/11/19/turkey-trouble-genetics-gone-too-far/turkeyfarm/\" rel=\"attachment wp-att-47026\">\u003cimg class=\"size-full wp-image-47026\" title=\"TurkeyFarm\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/11/TurkeyFarm.jpg\" alt=\"\" width=\"640\" height=\"356\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/11/TurkeyFarm.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/11/TurkeyFarm-400x223.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We've bred these poor things to the point where they can't even reproduce anymore without our help.\u003c/figcaption>\u003c/figure>\n\u003cp>No, this isn’t a blog about genetically modified organisms -- that has been argued enough lately! Instead, in honor of Thanksgiving, I want to talk about regular old selective breeding and the monsters it can create: the industrial turkey, the main course at most dinner tables on Thursday.\u003c/p>\n\u003cp>What we have all conspired to do to this once noble bird is appallingly awful. In our drive for more healthy white meat, we have selected for giant versions of turkeys with grotesquely over-sized breasts. How over-sized? Their breasts are so big at this point that these poor things can’t successfully mate. Every industrial turkey was created by artificial insemination.\u003c/p>\n\u003cp>Not only that, but all of that extra muscle has created birds in constant pain. Their bones just can’t easily handle all of that muscle being packed on so quickly. Add the damage to their hearts and the resulting high rate of heart attacks and you have something pretty close to monstrous.\u003c/p>\n\u003cp>And remember, we didn’t engineer these things at all. These caricatures of wild turkeys were hidden in the turkey genome all along.\u003c/p>\n\u003cp>Most species have an incredible amount of variation prepacked into their genomes. Look at a Great Dane and a Chihuahua and you’ll know what I mean! Both came from the same basic set of recipes, the wolf genome.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Wild turkeys have a wide range of possible turkeys hidden in their genome too. The current industrial turkey is just a certain combination of all of the different gene versions (or alleles) that were already present.\u003c/p>\n\u003cfigure id=\"attachment_47031\" class=\"wp-caption alignright\" style=\"max-width: 170px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/11/19/turkey-trouble-genetics-gone-too-far/goldenretriever/\" rel=\"attachment wp-att-47031\">\u003cimg class=\"size-full wp-image-47031\" title=\"GoldenRetriever\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/11/GoldenRetriever.jpg\" alt=\"\" width=\"170\" height=\"267\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">It doesn't just stop at turkeys either. Breeding for specific traits affects other animals too.\u003c/figcaption>\u003c/figure>\n\u003cp>Of course, if nature had stumbled on this particular combination of alleles in the wild, the resulting turkey would not have survived. Even if it managed to avoid bone damage and heart attacks, the thing couldn't successfully breed anyway. No, this turkey would have mercifully died out.\u003c/p>\n\u003cp>The situation is different on the factory farm. There the traits which would have doomed this turkey are selected for and this turkey ends up the “winner.” There are definitely different pressures in natural and artificial selection!\u003c/p>\n\u003cp>All of this raises the obvious ethical question. Just because we can breed this turkey, should we? The turkey lives a short, miserable life but we get an affordable, healthy source of protein. It is obvious which choice we’ve made as a society, but is it the right one?\u003c/p>\n\u003cp>And of course this discussion shouldn’t stop at the turkey. Chickens are having heart attacks all over the place, golden retrievers have a \u003ca href=\"http://genetics.thetech.org/ask/ask449\">ridiculously high rate of cancer\u003c/a>, and so on for many other artificially selected animals. Should we let this continue so we can have cheaper meat or a dog that looks just so?\u003c/p>\n\u003cp>Before ending, I do want to say that I am not opposed to all artificial selection. Without it, we’d have very few of the crops we have now. Our corn wouldn’t be as sweet, our grapes and bananas would have seeds and so on. It is just that we might want to be more careful in what we create. Especially when we tinker with animals.\u003c/p>\n\u003cp>\u003cstrong>Additional Reading:\u003c/strong>\u003c/p>\n\u003cp>\u003ca href=\"http://www.wired.com/wiredscience/2008/11/turkeytech/\">Great Wired Science Article on the Topic\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://ps.fass.org/content/77/12/1773.long\">Article on problems associated with rapid growth\u003c/a>\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/47023/turkey-trouble-genetics-gone-too-far","authors":["6177"],"categories":["quest_4","quest_3229"],"tags":["quest_1197","quest_13202","quest_11604","quest_13364","quest_2912","quest_3319","quest_3007"],"featImg":"quest_47026","label":"quest"},"quest_44236":{"type":"posts","id":"quest_44236","meta":{"index":"posts_1591205157","site":"quest","id":"44236","score":null,"sort":[1348498842000]},"guestAuthors":[],"slug":"genome-3-0-encode-takes-our-dna-from-junk-to-treasure","title":"Genome 3.0: ENCODE Takes Our DNA From Junk to Treasure","publishDate":1348498842,"format":"aside","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_44240\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/oasis/\" rel=\"attachment wp-att-44240\">\u003cimg class=\"size-full wp-image-44240\" title=\"Oasis\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/Oasis.jpg\" alt=\"\" width=\"640\" height=\"363\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/09/Oasis.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/Oasis-400x227.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Genes are not embedded in a vast expanse of junk DNA. Over 80% of our DNA appears to be doing something, somewhere, some time.\u003c/figcaption>\u003c/figure>\n\u003cp>New \u003ca href=\"http://www.nature.com/nature/journal/v489/n7414/full/489052a.html\">research\u003c/a> is making us rethink how our DNA works. Again.\u003c/p>\n\u003cp>Instead of a barren landscape dotted with the occasional gene, we now have a lush forest dotted with the occasional gene. This is the next step in our continuing evolution away from the idea that genes determine who we are to the determining factor being how we use the genes we have.\u003c/p>\n\u003cp>This new work from the ENCODE projects suggests that over 80% of our DNA is doing something even though only about 2% is genes. A lot of that something appears to be controlling when genes are turned on and to what level. At least that is what we think now.\u003c/p>\n\u003cp>Who knows what our new understanding will be once we come up with new ways to investigate what is going on in our DNA. And once we come up with the right questions to ask.\u003c/p>\n\u003cfigure id=\"attachment_44245\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/bacteria/\" rel=\"attachment wp-att-44245\">\u003cimg class=\"size-full wp-image-44245\" title=\"bacteria\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/bacteria.jpg\" alt=\"\" width=\"200\" height=\"168\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Not surprisingly, we use our DNA differently than a bacterium uses its DNA.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Genome 1.0\u003c/strong>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>In the beginning, there were genes. From work mostly in bacteria, scientists believed that these pieces of DNA were the key to who we were. And that what made us more complex than a bacterium or a water bug was that we had more genes.\u003c/p>\n\u003cp>This wasn’t crazy or anything. Given what they knew, genes seemed like the obvious candidates for making us who we are.\u003c/p>\n\u003cp>Remember, genes are just the instructions for proteins and proteins are the molecules that do the heavy lifting in our cells. The idea was that more complex creatures would do more things and so would need more proteins and so have more genes.\u003c/p>\n\u003cp>Scientists figured we’d be a bit like the bacteria they were studying. The thinking was that since by and large bacterial genomes are mostly genes, ours should be too. But once we managed to develop the technology to sequence the human genome, we saw that we don’t resemble bacteria nearly as much as we thought.\u003c/p>\n\u003cp>\u003cstrong>Genome 2.0\u003c/strong>\u003c/p>\n\u003cp>At the beginning of the 21st century, scientists sequenced the human genome. To everyone’s surprise there were only something like 20,000 – 25,000 genes. Most scientists expected 100,000 or more.\u003c/p>\n\u003cfigure id=\"attachment_44246\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/waterflea/\" rel=\"attachment wp-att-44246\">\u003cimg class=\"size-full wp-image-44246\" title=\"waterFlea\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/waterFlea.jpg\" alt=\"\" width=\"250\" height=\"250\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea.jpg 250w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-32x32.jpg 32w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-64x64.jpg 64w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-96x96.jpg 96w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-128x128.jpg 128w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-75x75.jpg 75w\" sizes=\"(max-width: 250px) 100vw, 250px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">She has more genes than you do.\u003cbr>Courtesy PLOS Genetics.\u003c/figcaption>\u003c/figure>\n\u003cp>The genome appeared to be long stretches of not-genes interspersed with the occasional gene. Given our still \u003cem>gene-ocentric\u003c/em> way of thinking, we called all the DNA that wasn’t a gene “junk” DNA. We figured it was the flotsam and jetsam of billions of years of evolution cluttering up our genomes.\u003c/p>\n\u003cp>As more and more organisms were sequenced, scientists kept getting the same result. Ten to thirty thousand genes spread across vast stretches of what looked like junk DNA. And to make matters worse, gene number didn’t appear to relate to complexity.\u003c/p>\n\u003cp>For example, a water flea has around \u003ca href=\"http://earthsky.org/earth/winner-for-largest-number-of-genes-in-any-animal-known-so-far-a-water-flea\">8,000 more genes than you do\u003c/a>. A mouse, roundworm and a flowering plant called \u003cem>Arabadopsis \u003c/em>has the same number as you. At least a fruit fly only has 14,000 or so! Clearly there isn’t a lot of correlation between complexity and gene number.\u003c/p>\n\u003cp>The current theory for what is going on is that the key factor in making us complex is how we use the genes we have. A mouse uses its 23,000 genes one way, roundworms another and humans a third way. Or more accurately, each uses its genes in lots of different ways depending on cell type, DNA sequence, environment and so on.\u003c/p>\n\u003cp>The ENCODE project appears to support this idea and to show that a lot of that junk DNA is actually involved in controlling genes. One man’s junk is another man’s treasure.\u003c/p>\n\u003cp>\u003cstrong>Genome 3.0\u003c/strong>\u003c/p>\n\u003cp>The ENCODE project set out to figure out how genes are controlled. They focused on proteins called transcription factors (TFs) because scientists already had a pretty good handle on how these things work.\u003c/p>\n\u003cfigure id=\"attachment_44251\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/tbp/\" rel=\"attachment wp-att-44251\">\u003cimg class=\"size-full wp-image-44251\" title=\"TBP\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/TBP.jpg\" alt=\"\" width=\"200\" height=\"147\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Transcription factors like this one are proteins that bind DNA and control how much a gene is turned on.\u003c/figcaption>\u003c/figure>\n\u003cp>TFs stick to certain bits of DNA and control genes from there. So one might like the DNA sequence AAGCTT and another might like TATAAA. Each TF then sticks to any of its preferred sites that are accessible and the level of gene expression is determined by which factors are bound where for how long.\u003c/p>\n\u003cp>The ENCODE project found way more of these TF binding sites than they thought they would. And while they matched up half a million to nearby genes, this still left millions that were without a gene. They are almost certainly controlling genes, we just don’t yet understand how.\u003c/p>\n\u003cp>One way they are probably controlling genes is through some sort of long distance control. Scientists already knew of many cases where DNA far from a gene can influence its expression. (And when I say far, I mean far. Our chromosome 1 is over 3 inches long on its own. That is massive in the microscopic world. If the nucleus where the DNA is stored was the size of a baseball, the DNA of chromsome 1 would be over 100 miles long. That is quite a bat!)\u003c/p>\n\u003cp>One way this long distance control is thought to happen has to do with the fact that this long molecule isn’t stretched out. Instead it is packaged in an ordered clump.\u003c/p>\n\u003cp>So even though those TFs I talked about are arranged along these long molecules sort of like beads on a string, pieces that are far away on the DNA can be close in 3D space. Members of the ENCODE project identified and analyzed over 1000 of these DNA loops.\u003c/p>\n\u003cp>Another way to influence gene expression is by affecting the accessibility of the TF binding sites on the DNA. If a site is hidden, it can’t be bound by a TF and so can’t affect any genes.\u003c/p>\n\u003cp>Accessibility is controlled by that packaging (chromatin) I talked about earlier. Some DNA is in parts of the clump that the TFs can get to and some isn’t.\u003c/p>\n\u003cfigure id=\"attachment_44269\" class=\"wp-caption alignleft\" style=\"max-width: 100px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/chromatin/\" rel=\"attachment wp-att-44269\">\u003cimg class=\"size-full wp-image-44269\" title=\"chromatin\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/chromatin.jpg\" alt=\"\" width=\"100\" height=\"246\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">TFs have to get to the DNA to have an effect.\u003c/figcaption>\u003c/figure>\n\u003cp>Another ENCODE group determined how the pattern of accessibility is different in different cell types and firmed up the idea that TF binding can be like an avalanche. One TF binds which opens the DNA up allowing more to bind which opens up more DNA and so on.\u003c/p>\n\u003cp>Among its many contributions, the ENCODE data provides us with the start of a cataloging of what parts of our DNA are important and, to a lesser extent, which parts interact with each other. This data is already starting to bear fruit in that it is providing us with clues to how certain genetic differences can affect a person’s chances for developing genetic diseases. In particular, certain findings with regard to Crohn’s disease are becoming more understandable.\u003c/p>\n\u003cp>The results I’ve described so far aren’t really a paradigm shift except in terms of the percentage of DNA being used. It is things any molecular biologist knew before just spread out over more of our DNA and described in much more detail. This is not true of all of the results though.\u003c/p>\n\u003cp>Another big finding of the ENCODE project is that over 75% of our DNA is copied into RNA in one cell or another. This was unexpected and might one day push us to \u003cem>Genome 4.0\u003c/em>.\u003c/p>\n\u003cp>You may remember that genes are copied into RNA before they are translated into proteins. Given that only 2% of our DNA is genes, all this RNA is not being translated into proteins. Which given what we’ve learned over the past few years, isn’t unexpected.\u003c/p>\n\u003cp>Scientists had been finding lots of different RNAs involved in, you guessed it, controlling gene expression levels. But no one expected there was this much untranslated RNA. There is so much of it that it is unlikely it is all contributing to controlling genes in the ways we’ve identified so far.\u003c/p>\n\u003cp>No, there are still lots of things to find out and when they figure out what this RNA is doing, we’ll learn more about our genomes. And I can’t wait to see what else they find as they’re figuring it out.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>\u003ca href=\"http://modencode.sciencemag.org\">An educational site about the related modENCODE project (still at the beta stage)\u003c/a>\u003c/p>\n\n","blocks":[],"excerpt":"New research is making us rethink how our DNA works - again.","status":"publish","parent":0,"modified":1349809216,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":35,"wordCount":1452},"headData":{"title":"Genome 3.0: ENCODE Takes Our DNA From Junk to Treasure | KQED","description":"New research is making us rethink how our DNA works - again.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"44236 http://science.kqed.org/quest/?p=44236","disqusUrl":"https://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/","disqusTitle":"Genome 3.0: ENCODE Takes Our DNA From Junk to Treasure","path":"/quest/44236/genome-3-0-encode-takes-our-dna-from-junk-to-treasure","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_44240\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/oasis/\" rel=\"attachment wp-att-44240\">\u003cimg class=\"size-full wp-image-44240\" title=\"Oasis\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/Oasis.jpg\" alt=\"\" width=\"640\" height=\"363\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/09/Oasis.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/Oasis-400x227.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Genes are not embedded in a vast expanse of junk DNA. Over 80% of our DNA appears to be doing something, somewhere, some time.\u003c/figcaption>\u003c/figure>\n\u003cp>New \u003ca href=\"http://www.nature.com/nature/journal/v489/n7414/full/489052a.html\">research\u003c/a> is making us rethink how our DNA works. Again.\u003c/p>\n\u003cp>Instead of a barren landscape dotted with the occasional gene, we now have a lush forest dotted with the occasional gene. This is the next step in our continuing evolution away from the idea that genes determine who we are to the determining factor being how we use the genes we have.\u003c/p>\n\u003cp>This new work from the ENCODE projects suggests that over 80% of our DNA is doing something even though only about 2% is genes. A lot of that something appears to be controlling when genes are turned on and to what level. At least that is what we think now.\u003c/p>\n\u003cp>Who knows what our new understanding will be once we come up with new ways to investigate what is going on in our DNA. And once we come up with the right questions to ask.\u003c/p>\n\u003cfigure id=\"attachment_44245\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/bacteria/\" rel=\"attachment wp-att-44245\">\u003cimg class=\"size-full wp-image-44245\" title=\"bacteria\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/bacteria.jpg\" alt=\"\" width=\"200\" height=\"168\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Not surprisingly, we use our DNA differently than a bacterium uses its DNA.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Genome 1.0\u003c/strong>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>In the beginning, there were genes. From work mostly in bacteria, scientists believed that these pieces of DNA were the key to who we were. And that what made us more complex than a bacterium or a water bug was that we had more genes.\u003c/p>\n\u003cp>This wasn’t crazy or anything. Given what they knew, genes seemed like the obvious candidates for making us who we are.\u003c/p>\n\u003cp>Remember, genes are just the instructions for proteins and proteins are the molecules that do the heavy lifting in our cells. The idea was that more complex creatures would do more things and so would need more proteins and so have more genes.\u003c/p>\n\u003cp>Scientists figured we’d be a bit like the bacteria they were studying. The thinking was that since by and large bacterial genomes are mostly genes, ours should be too. But once we managed to develop the technology to sequence the human genome, we saw that we don’t resemble bacteria nearly as much as we thought.\u003c/p>\n\u003cp>\u003cstrong>Genome 2.0\u003c/strong>\u003c/p>\n\u003cp>At the beginning of the 21st century, scientists sequenced the human genome. To everyone’s surprise there were only something like 20,000 – 25,000 genes. Most scientists expected 100,000 or more.\u003c/p>\n\u003cfigure id=\"attachment_44246\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/waterflea/\" rel=\"attachment wp-att-44246\">\u003cimg class=\"size-full wp-image-44246\" title=\"waterFlea\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/waterFlea.jpg\" alt=\"\" width=\"250\" height=\"250\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea.jpg 250w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-32x32.jpg 32w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-64x64.jpg 64w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-96x96.jpg 96w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-128x128.jpg 128w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/waterFlea-75x75.jpg 75w\" sizes=\"(max-width: 250px) 100vw, 250px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">She has more genes than you do.\u003cbr>Courtesy PLOS Genetics.\u003c/figcaption>\u003c/figure>\n\u003cp>The genome appeared to be long stretches of not-genes interspersed with the occasional gene. Given our still \u003cem>gene-ocentric\u003c/em> way of thinking, we called all the DNA that wasn’t a gene “junk” DNA. We figured it was the flotsam and jetsam of billions of years of evolution cluttering up our genomes.\u003c/p>\n\u003cp>As more and more organisms were sequenced, scientists kept getting the same result. Ten to thirty thousand genes spread across vast stretches of what looked like junk DNA. And to make matters worse, gene number didn’t appear to relate to complexity.\u003c/p>\n\u003cp>For example, a water flea has around \u003ca href=\"http://earthsky.org/earth/winner-for-largest-number-of-genes-in-any-animal-known-so-far-a-water-flea\">8,000 more genes than you do\u003c/a>. A mouse, roundworm and a flowering plant called \u003cem>Arabadopsis \u003c/em>has the same number as you. At least a fruit fly only has 14,000 or so! Clearly there isn’t a lot of correlation between complexity and gene number.\u003c/p>\n\u003cp>The current theory for what is going on is that the key factor in making us complex is how we use the genes we have. A mouse uses its 23,000 genes one way, roundworms another and humans a third way. Or more accurately, each uses its genes in lots of different ways depending on cell type, DNA sequence, environment and so on.\u003c/p>\n\u003cp>The ENCODE project appears to support this idea and to show that a lot of that junk DNA is actually involved in controlling genes. One man’s junk is another man’s treasure.\u003c/p>\n\u003cp>\u003cstrong>Genome 3.0\u003c/strong>\u003c/p>\n\u003cp>The ENCODE project set out to figure out how genes are controlled. They focused on proteins called transcription factors (TFs) because scientists already had a pretty good handle on how these things work.\u003c/p>\n\u003cfigure id=\"attachment_44251\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/tbp/\" rel=\"attachment wp-att-44251\">\u003cimg class=\"size-full wp-image-44251\" title=\"TBP\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/TBP.jpg\" alt=\"\" width=\"200\" height=\"147\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Transcription factors like this one are proteins that bind DNA and control how much a gene is turned on.\u003c/figcaption>\u003c/figure>\n\u003cp>TFs stick to certain bits of DNA and control genes from there. So one might like the DNA sequence AAGCTT and another might like TATAAA. Each TF then sticks to any of its preferred sites that are accessible and the level of gene expression is determined by which factors are bound where for how long.\u003c/p>\n\u003cp>The ENCODE project found way more of these TF binding sites than they thought they would. And while they matched up half a million to nearby genes, this still left millions that were without a gene. They are almost certainly controlling genes, we just don’t yet understand how.\u003c/p>\n\u003cp>One way they are probably controlling genes is through some sort of long distance control. Scientists already knew of many cases where DNA far from a gene can influence its expression. (And when I say far, I mean far. Our chromosome 1 is over 3 inches long on its own. That is massive in the microscopic world. If the nucleus where the DNA is stored was the size of a baseball, the DNA of chromsome 1 would be over 100 miles long. That is quite a bat!)\u003c/p>\n\u003cp>One way this long distance control is thought to happen has to do with the fact that this long molecule isn’t stretched out. Instead it is packaged in an ordered clump.\u003c/p>\n\u003cp>So even though those TFs I talked about are arranged along these long molecules sort of like beads on a string, pieces that are far away on the DNA can be close in 3D space. Members of the ENCODE project identified and analyzed over 1000 of these DNA loops.\u003c/p>\n\u003cp>Another way to influence gene expression is by affecting the accessibility of the TF binding sites on the DNA. If a site is hidden, it can’t be bound by a TF and so can’t affect any genes.\u003c/p>\n\u003cp>Accessibility is controlled by that packaging (chromatin) I talked about earlier. Some DNA is in parts of the clump that the TFs can get to and some isn’t.\u003c/p>\n\u003cfigure id=\"attachment_44269\" class=\"wp-caption alignleft\" style=\"max-width: 100px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/24/genome-3-0-encode-takes-our-dna-from-junk-to-treasure/chromatin/\" rel=\"attachment wp-att-44269\">\u003cimg class=\"size-full wp-image-44269\" title=\"chromatin\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/chromatin.jpg\" alt=\"\" width=\"100\" height=\"246\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">TFs have to get to the DNA to have an effect.\u003c/figcaption>\u003c/figure>\n\u003cp>Another ENCODE group determined how the pattern of accessibility is different in different cell types and firmed up the idea that TF binding can be like an avalanche. One TF binds which opens the DNA up allowing more to bind which opens up more DNA and so on.\u003c/p>\n\u003cp>Among its many contributions, the ENCODE data provides us with the start of a cataloging of what parts of our DNA are important and, to a lesser extent, which parts interact with each other. This data is already starting to bear fruit in that it is providing us with clues to how certain genetic differences can affect a person’s chances for developing genetic diseases. In particular, certain findings with regard to Crohn’s disease are becoming more understandable.\u003c/p>\n\u003cp>The results I’ve described so far aren’t really a paradigm shift except in terms of the percentage of DNA being used. It is things any molecular biologist knew before just spread out over more of our DNA and described in much more detail. This is not true of all of the results though.\u003c/p>\n\u003cp>Another big finding of the ENCODE project is that over 75% of our DNA is copied into RNA in one cell or another. This was unexpected and might one day push us to \u003cem>Genome 4.0\u003c/em>.\u003c/p>\n\u003cp>You may remember that genes are copied into RNA before they are translated into proteins. Given that only 2% of our DNA is genes, all this RNA is not being translated into proteins. Which given what we’ve learned over the past few years, isn’t unexpected.\u003c/p>\n\u003cp>Scientists had been finding lots of different RNAs involved in, you guessed it, controlling gene expression levels. But no one expected there was this much untranslated RNA. There is so much of it that it is unlikely it is all contributing to controlling genes in the ways we’ve identified so far.\u003c/p>\n\u003cp>No, there are still lots of things to find out and when they figure out what this RNA is doing, we’ll learn more about our genomes. And I can’t wait to see what else they find as they’re figuring it out.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://modencode.sciencemag.org\">An educational site about the related modENCODE project (still at the beta stage)\u003c/a>\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/44236/genome-3-0-encode-takes-our-dna-from-junk-to-treasure","authors":["6177"],"categories":["quest_4"],"tags":["quest_11455","quest_10466","quest_1197","quest_11456","quest_13202","quest_3319","quest_2978","quest_11457"],"featImg":"quest_44240","label":"quest"},"quest_43103":{"type":"posts","id":"quest_43103","meta":{"index":"posts_1591205157","site":"quest","id":"43103","score":null,"sort":[1347289255000]},"guestAuthors":[],"slug":"the-results-are-in-for-my-genetics-qui","title":"The Results Are In For My Genetics Quiz ","publishDate":1347289255,"format":"aside","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_43106\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/quiz1image/\" rel=\"attachment wp-att-43106\">\u003cimg class=\"size-full wp-image-43106\" title=\"Quiz1Image\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Quiz1Image.jpg\" alt=\"\" width=\"640\" height=\"369\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/08/Quiz1Image.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/Quiz1Image-400x231.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Lots of right answers from clever QUEST respondents!\u003c/figcaption>\u003c/figure>\n\u003cp>In my \u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/\" target=\"_blank\">last blog entry\u003c/a>, I wrote a quiz that tested some basic knowledge about genetics that experts have found the public struggles with. What I found from the responses I received is that the QUEST public doesn’t struggle with them or, more likely, people only answer quizzes like this if they are pretty confident in the first place. The ten respondents did very well indeed!\u003c/p>\n\u003cp>I also learned that I need to work on my question writing skills. In my efforts to be brief and to the point, I ended up writing the occasional question that had more than one correct answer. Of course once I realized that I scored either of the correct answers as correct.\u003c/p>\n\u003cp>What I’ll do below is go over each question in a bit more detail. I’ll talk about why I asked it and what the answer is.\u003c/p>\n\u003cp>\u003cem>1) Should you necessarily be scared if you find out you are 10 times more likely to get a rare cancer?\u003c/em>\u003c/p>\n\u003cp>The answer to this one is no, you should not be scared. Everyone got this one right.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>If 1 in a million people get a certain cancer, the increase to 1 in 100,000 is pretty minimal. It is equivalent to \u003ca href=\"http://www.funny2.com/odds.htm\">the difference between\u003c/a> getting struck by lightning and dating a supermodel. Neither is at all likely!\u003c/p>\n\u003cp>The reason I included this question is that \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945403/\">one of the studies\u003c/a> suggested that this is a pretty common problem for people getting genetic counseling. They struggle with the idea of absolute vs. relative risk. In other words, the difference between how much more likely I am to get a disease compared to you versus how likely I am to get a disease period.\u003c/p>\n\u003cfigure id=\"attachment_43125\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/motherdaughter/\" rel=\"attachment wp-att-43125\">\u003cimg class=\"size-full wp-image-43125\" title=\"MotherDaughter\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/MotherDaughter.jpg\" alt=\"\" width=\"150\" height=\"141\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Just because you look like mom that doesn't mean you'll necessarily end up with her family's diseases.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cem>2) If you look like your mom, are you more likely to get the diseases that run in her family or your dad’s family?\u003c/em>\u003c/p>\n\u003cp>The answer to this one is no as well. Nine out of ten respondents got this one right.\u003c/p>\n\u003cp>The few genes associated with looks have very little to do with disease risk. Just because you and your mom have blue eyes, this has nothing to do with whether you have your mom’s increased risk for type 2 diabetes. There are different genes associated with each and they are independent of one another.\u003c/p>\n\u003cp>Here is another example. Let’s say Huntington’s disease runs in your dad’s family and your dad has the version of the huntingtin gene that will lead to him getting the disease. Your chances of getting the disease are 50% whether or not you have mom’s blue eyes and blonde hair or dad’s brown eyes and hair. The disease and the traits are caused by different genes...they do not come as a package deal.\u003c/p>\n\u003cp>One of the exceptions would be red hair and fair skin. These traits, which are caused by certain versions of the MC1R gene, do increase a person’s risk for skin cancer.\u003c/p>\n\u003cp>I included this question because of the multitude of similar questions about this that I have received at \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist\">Ask a Geneticist\u003c/a> and because it is mentioned in the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945403/\">genetics counseling study\u003c/a>.\u003c/p>\n\u003cp>\u003cem>3) If you have the recessive disease sickle cell anemia, should your kids be tested to see if they are carriers?\u003c/em>\u003c/p>\n\u003cp>In the way I was thinking about the question, the answer would be no. Only one out of ten people got this right but I suspect that may have to do with how I wrote the question.\u003c/p>\n\u003cp>What I was trying to get at is if you have a recessive disease, then all of your kids will almost certainly be carriers of that disease. So there isn’t really any need for genetic testing.\u003c/p>\n\u003cp>Remember, we have two copies of each of our genes and for a recessive trait to be seen, both copies have to be the recessive version. Also remember that people pass one of their two copies of each gene to their child.\u003c/p>\n\u003cp>What this means is people with sickle cell anemia have to pass a version of the hemoglobin gene that can lead to sickle cell anemia down to each of their kids. All their kids will be carriers.\u003c/p>\n\u003cp>So a genetic test probably isn’t necessary for the kids because they are undoubtedly carriers. Now that doesn’t mean the other partner shouldn’t be tested. He or she definitely should be tested to determine his or her carrier status. This will affect their chances for having a child with sickle cell anemia.\u003c/p>\n\u003cp>I included this question because both the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945403/\">genetic counseling\u003c/a> and the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/19039252\">Australian\u003c/a> study showed that the idea of dominant and recessive traits was a confusing one. This also bears out in our list of \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist\">Ask a Geneticist\u003c/a> questions.\u003c/p>\n\u003cfigure id=\"attachment_43115\" class=\"wp-caption alignright\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/cuteredheadedbaby/\" rel=\"attachment wp-att-43115\">\u003cimg class=\"size-full wp-image-43115\" title=\"CuteRedheadedBaby\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/CuteRedheadedBaby.gif\" alt=\"\" width=\"250\" height=\"188\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Sometimes to look like one parent, you need genes from both! Red hair is one of these.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cem>4) If you look like your dad, did you get more of his DNA?\u003c/em>\u003c/p>\n\u003cp>The answer here is a definite no. People almost always get half their DNA from their mom and half from their dad no matter who they look like. (Click \u003ca href=\"http://genetics.thetech.org/ask/ask289\">here\u003c/a>, \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist/paternal-grandmothers-dna\">here \u003c/a>and \u003ca href=\"http://genetics.thetech.org/ask/ask435\">here \u003c/a>for some exceptions to this rule.) Eight out of ten people got this question right.\u003c/p>\n\u003cp>Again we have the issue where what we look like comes from only a few genes. Looking like your dad might mean you happened to get 20 or 50 of his genes related to physical appearance. This is out of the 25,000 or so genes we all have.\u003c/p>\n\u003cp>In fact, there are even some traits where you look like one parent because both parents contributed the right DNA. Let’s say you and your dad are a redhead. It is very unlikely you have red hair only because of him because red hair is a recessive trait and usually has to come from both sides of the family. In other words, mom had to pass you a red hair version of MC1R so you could look like your dad!\u003c/p>\n\u003cp>\u003cem>5) If you flip a coin and get heads ten times in a row, what are the chances that the next flip will be a head?\u003c/em>\u003c/p>\n\u003cp>The answer is 50%. Each coin flip is independent so what came before cannot affect the next flip. The coin doesn’t remember on which side it landed before. Nine out of ten got this one right.\u003c/p>\n\u003cp>It is a very common misconception that if you flip a coin and get ten heads in a row, the next flip is more likely to be a tail (it is due!). Heck, my dad plays the craps tables in Las Vegas by looking for tables where a seven hasn’t come up in a while and places his bets at that table. This is no way to win.\u003c/p>\n\u003cp>In genetics this mostly becomes an issue in predicting a child’s traits based on the children that came before. If two parents have four girls, they might think that a boy is more likely next time around. And if both parents are carriers for cystic fibrosis (CF), they might feel that if they’ve already had a child with CF, the risk is decreased for the next child. After all, that Punnett square showed that 1 in 4 of their kids would have CF, right? Well, no.\u003c/p>\n\u003cp>The Punnett square was used to calculate the risk that each child has for getting CF. If your first child has CF, your second still has a 1 in 4 chance for getting CF. Just because your first got it, that does not affect your second child’s chances.\u003c/p>\n\u003cfigure id=\"attachment_43120\" class=\"wp-caption alignright\" style=\"max-width: 100px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/dna/\" rel=\"attachment wp-att-43120\">\u003cimg class=\"size-full wp-image-43120\" title=\"DNA\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/DNA.jpg\" alt=\"\" width=\"100\" height=\"250\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Cells look different because they use different parts of the same DNA.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cem>6) True or false: Each cell in your body has the same DNA.\u003c/em>\u003c/p>\n\u003cp>OK, this is the question I messed up on big time. By trying to keep it short and sweet, I didn’t ask the right question. What I should have asked was:\u003c/p>\n\u003cp>\u003cem>A muscle and a brain cell have the same DNA. True or False\u003c/em>\u003c/p>\n\u003cp>The answer to that question is “True” and we could have a nice discussion about how most of the cells in our body have the exact same DNA even though they look different. And then I’d go on to talk about how the differences come from the fact that each cell uses a different subset of genes. Sort of like following a single recipe in a cookbook to make cookies instead of following every recipe.\u003c/p>\n\u003cp>But alas, I asked the wrong question and most of the respondents correctly noted the exceptions to the “every cell has the same DNA” idea. They noted that sperm and eggs have half the usual amount of DNA. And that because of mutations, various cells in our bodies have small differences from one another. They also mentioned that we are actually composed of our cells plus the trillions of bacteria that we all carry. (No one mentioned mature red blood cells which have no DNA.)\u003c/p>\n\u003cp>I hope you enjoyed the quiz and that you’ll enjoy the book, \u003ca href=\"http://genetics.thetech.org/book-titles\">When Will Broccoli Taste Like Chocolate?\u003c/a>. I am happy to do more quizzes like this in the future if people are interested. Any suggestions on genetics topics?\u003c/p>\n\u003cp>\u003cem>More scary news:\u003c/em>\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/yikes/\" rel=\"attachment wp-att-43256\">\u003cimg class=\"aligncenter size-full wp-image-43256\" title=\"Yikes\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/Yikes.jpg\" alt=\"\" width=\"434\" height=\"552\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/09/Yikes.jpg 434w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/Yikes-400x509.jpg 400w\" sizes=\"(max-width: 434px) 100vw, 434px\">\u003c/a> Click \u003ca href=\"http://www.facebook.com/photo.php?fbid=465671563453860&set=a.456449604376056.98921.367116489976035&type=1&theater\">here \u003c/a>for source.\u003c/p>\n\n","blocks":[],"excerpt":null,"status":"publish","parent":0,"modified":1346358464,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":39,"wordCount":1612},"headData":{"title":"The Results Are In For My Genetics Quiz | KQED","description":"In my last blog entry, I wrote a quiz that tested some basic knowledge about genetics that experts have found the public struggles with. What I found from the responses I received is that the QUEST public doesn’t struggle with them or, more likely, people only answer quizzes like this if they are pretty confident","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"43103 http://science.kqed.org/quest/?p=43103","disqusUrl":"https://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/","disqusTitle":"The Results Are In For My Genetics Quiz ","path":"/quest/43103/the-results-are-in-for-my-genetics-qui","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_43106\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/quiz1image/\" rel=\"attachment wp-att-43106\">\u003cimg class=\"size-full wp-image-43106\" title=\"Quiz1Image\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Quiz1Image.jpg\" alt=\"\" width=\"640\" height=\"369\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/08/Quiz1Image.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/Quiz1Image-400x231.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Lots of right answers from clever QUEST respondents!\u003c/figcaption>\u003c/figure>\n\u003cp>In my \u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/\" target=\"_blank\">last blog entry\u003c/a>, I wrote a quiz that tested some basic knowledge about genetics that experts have found the public struggles with. What I found from the responses I received is that the QUEST public doesn’t struggle with them or, more likely, people only answer quizzes like this if they are pretty confident in the first place. The ten respondents did very well indeed!\u003c/p>\n\u003cp>I also learned that I need to work on my question writing skills. In my efforts to be brief and to the point, I ended up writing the occasional question that had more than one correct answer. Of course once I realized that I scored either of the correct answers as correct.\u003c/p>\n\u003cp>What I’ll do below is go over each question in a bit more detail. I’ll talk about why I asked it and what the answer is.\u003c/p>\n\u003cp>\u003cem>1) Should you necessarily be scared if you find out you are 10 times more likely to get a rare cancer?\u003c/em>\u003c/p>\n\u003cp>The answer to this one is no, you should not be scared. Everyone got this one right.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>If 1 in a million people get a certain cancer, the increase to 1 in 100,000 is pretty minimal. It is equivalent to \u003ca href=\"http://www.funny2.com/odds.htm\">the difference between\u003c/a> getting struck by lightning and dating a supermodel. Neither is at all likely!\u003c/p>\n\u003cp>The reason I included this question is that \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945403/\">one of the studies\u003c/a> suggested that this is a pretty common problem for people getting genetic counseling. They struggle with the idea of absolute vs. relative risk. In other words, the difference between how much more likely I am to get a disease compared to you versus how likely I am to get a disease period.\u003c/p>\n\u003cfigure id=\"attachment_43125\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/motherdaughter/\" rel=\"attachment wp-att-43125\">\u003cimg class=\"size-full wp-image-43125\" title=\"MotherDaughter\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/MotherDaughter.jpg\" alt=\"\" width=\"150\" height=\"141\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Just because you look like mom that doesn't mean you'll necessarily end up with her family's diseases.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cem>2) If you look like your mom, are you more likely to get the diseases that run in her family or your dad’s family?\u003c/em>\u003c/p>\n\u003cp>The answer to this one is no as well. Nine out of ten respondents got this one right.\u003c/p>\n\u003cp>The few genes associated with looks have very little to do with disease risk. Just because you and your mom have blue eyes, this has nothing to do with whether you have your mom’s increased risk for type 2 diabetes. There are different genes associated with each and they are independent of one another.\u003c/p>\n\u003cp>Here is another example. Let’s say Huntington’s disease runs in your dad’s family and your dad has the version of the huntingtin gene that will lead to him getting the disease. Your chances of getting the disease are 50% whether or not you have mom’s blue eyes and blonde hair or dad’s brown eyes and hair. The disease and the traits are caused by different genes...they do not come as a package deal.\u003c/p>\n\u003cp>One of the exceptions would be red hair and fair skin. These traits, which are caused by certain versions of the MC1R gene, do increase a person’s risk for skin cancer.\u003c/p>\n\u003cp>I included this question because of the multitude of similar questions about this that I have received at \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist\">Ask a Geneticist\u003c/a> and because it is mentioned in the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945403/\">genetics counseling study\u003c/a>.\u003c/p>\n\u003cp>\u003cem>3) If you have the recessive disease sickle cell anemia, should your kids be tested to see if they are carriers?\u003c/em>\u003c/p>\n\u003cp>In the way I was thinking about the question, the answer would be no. Only one out of ten people got this right but I suspect that may have to do with how I wrote the question.\u003c/p>\n\u003cp>What I was trying to get at is if you have a recessive disease, then all of your kids will almost certainly be carriers of that disease. So there isn’t really any need for genetic testing.\u003c/p>\n\u003cp>Remember, we have two copies of each of our genes and for a recessive trait to be seen, both copies have to be the recessive version. Also remember that people pass one of their two copies of each gene to their child.\u003c/p>\n\u003cp>What this means is people with sickle cell anemia have to pass a version of the hemoglobin gene that can lead to sickle cell anemia down to each of their kids. All their kids will be carriers.\u003c/p>\n\u003cp>So a genetic test probably isn’t necessary for the kids because they are undoubtedly carriers. Now that doesn’t mean the other partner shouldn’t be tested. He or she definitely should be tested to determine his or her carrier status. This will affect their chances for having a child with sickle cell anemia.\u003c/p>\n\u003cp>I included this question because both the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945403/\">genetic counseling\u003c/a> and the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/19039252\">Australian\u003c/a> study showed that the idea of dominant and recessive traits was a confusing one. This also bears out in our list of \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist\">Ask a Geneticist\u003c/a> questions.\u003c/p>\n\u003cfigure id=\"attachment_43115\" class=\"wp-caption alignright\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/cuteredheadedbaby/\" rel=\"attachment wp-att-43115\">\u003cimg class=\"size-full wp-image-43115\" title=\"CuteRedheadedBaby\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/CuteRedheadedBaby.gif\" alt=\"\" width=\"250\" height=\"188\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Sometimes to look like one parent, you need genes from both! Red hair is one of these.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cem>4) If you look like your dad, did you get more of his DNA?\u003c/em>\u003c/p>\n\u003cp>The answer here is a definite no. People almost always get half their DNA from their mom and half from their dad no matter who they look like. (Click \u003ca href=\"http://genetics.thetech.org/ask/ask289\">here\u003c/a>, \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist/paternal-grandmothers-dna\">here \u003c/a>and \u003ca href=\"http://genetics.thetech.org/ask/ask435\">here \u003c/a>for some exceptions to this rule.) Eight out of ten people got this question right.\u003c/p>\n\u003cp>Again we have the issue where what we look like comes from only a few genes. Looking like your dad might mean you happened to get 20 or 50 of his genes related to physical appearance. This is out of the 25,000 or so genes we all have.\u003c/p>\n\u003cp>In fact, there are even some traits where you look like one parent because both parents contributed the right DNA. Let’s say you and your dad are a redhead. It is very unlikely you have red hair only because of him because red hair is a recessive trait and usually has to come from both sides of the family. In other words, mom had to pass you a red hair version of MC1R so you could look like your dad!\u003c/p>\n\u003cp>\u003cem>5) If you flip a coin and get heads ten times in a row, what are the chances that the next flip will be a head?\u003c/em>\u003c/p>\n\u003cp>The answer is 50%. Each coin flip is independent so what came before cannot affect the next flip. The coin doesn’t remember on which side it landed before. Nine out of ten got this one right.\u003c/p>\n\u003cp>It is a very common misconception that if you flip a coin and get ten heads in a row, the next flip is more likely to be a tail (it is due!). Heck, my dad plays the craps tables in Las Vegas by looking for tables where a seven hasn’t come up in a while and places his bets at that table. This is no way to win.\u003c/p>\n\u003cp>In genetics this mostly becomes an issue in predicting a child’s traits based on the children that came before. If two parents have four girls, they might think that a boy is more likely next time around. And if both parents are carriers for cystic fibrosis (CF), they might feel that if they’ve already had a child with CF, the risk is decreased for the next child. After all, that Punnett square showed that 1 in 4 of their kids would have CF, right? Well, no.\u003c/p>\n\u003cp>The Punnett square was used to calculate the risk that each child has for getting CF. If your first child has CF, your second still has a 1 in 4 chance for getting CF. Just because your first got it, that does not affect your second child’s chances.\u003c/p>\n\u003cfigure id=\"attachment_43120\" class=\"wp-caption alignright\" style=\"max-width: 100px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/dna/\" rel=\"attachment wp-att-43120\">\u003cimg class=\"size-full wp-image-43120\" title=\"DNA\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/DNA.jpg\" alt=\"\" width=\"100\" height=\"250\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Cells look different because they use different parts of the same DNA.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cem>6) True or false: Each cell in your body has the same DNA.\u003c/em>\u003c/p>\n\u003cp>OK, this is the question I messed up on big time. By trying to keep it short and sweet, I didn’t ask the right question. What I should have asked was:\u003c/p>\n\u003cp>\u003cem>A muscle and a brain cell have the same DNA. True or False\u003c/em>\u003c/p>\n\u003cp>The answer to that question is “True” and we could have a nice discussion about how most of the cells in our body have the exact same DNA even though they look different. And then I’d go on to talk about how the differences come from the fact that each cell uses a different subset of genes. Sort of like following a single recipe in a cookbook to make cookies instead of following every recipe.\u003c/p>\n\u003cp>But alas, I asked the wrong question and most of the respondents correctly noted the exceptions to the “every cell has the same DNA” idea. They noted that sperm and eggs have half the usual amount of DNA. And that because of mutations, various cells in our bodies have small differences from one another. They also mentioned that we are actually composed of our cells plus the trillions of bacteria that we all carry. (No one mentioned mature red blood cells which have no DNA.)\u003c/p>\n\u003cp>I hope you enjoyed the quiz and that you’ll enjoy the book, \u003ca href=\"http://genetics.thetech.org/book-titles\">When Will Broccoli Taste Like Chocolate?\u003c/a>. I am happy to do more quizzes like this in the future if people are interested. Any suggestions on genetics topics?\u003c/p>\n\u003cp>\u003cem>More scary news:\u003c/em>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2012/09/10/the-results-are-in-for-my-genetics-qui/yikes/\" rel=\"attachment wp-att-43256\">\u003cimg class=\"aligncenter size-full wp-image-43256\" title=\"Yikes\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/09/Yikes.jpg\" alt=\"\" width=\"434\" height=\"552\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/09/Yikes.jpg 434w, https://ww2.kqed.org/app/uploads/sites/39/2012/09/Yikes-400x509.jpg 400w\" sizes=\"(max-width: 434px) 100vw, 434px\">\u003c/a> Click \u003ca href=\"http://www.facebook.com/photo.php?fbid=465671563453860&set=a.456449604376056.98921.367116489976035&type=1&theater\">here \u003c/a>for source.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/43103/the-results-are-in-for-my-genetics-qui","authors":["6177"],"categories":["quest_4","quest_12"],"tags":["quest_11395","quest_3549","quest_11183","quest_1197","quest_11397","quest_13202","quest_3733","quest_11396","quest_3319"],"featImg":"quest_43106","label":"quest"},"quest_22785":{"type":"posts","id":"quest_22785","meta":{"index":"posts_1591205157","site":"quest","id":"22785","score":null,"sort":[1346774404000]},"guestAuthors":[],"slug":"heat-is-on-for-california-wines","title":"The Heat is On For California Wines","publishDate":1346774404,"format":"audio","headTitle":"Heat and Harvest | QUEST | KQED Science","labelTerm":{},"content":"\u003cp>You've probably heard of the wines that made Napa and Sonoma famous, like Cabernet Sauvignon or Chardonnay. But what about \u003ca href=\"http://en.wikipedia.org/wiki/Negroamaro\">Negroamaro\u003c/a> or \u003ca href=\"http://en.wikipedia.org/wiki/Nero_d%27Avola\">Nero d'Avola\u003c/a>?\u003c/p>\n\u003cp>They're wine grapes that are well-adapted to hotter climates – the kind of conditions that California may be facing as the climate continues to warm. But for wineries that have staked their reputations on certain wines, adapting to climate change could be a tough sell.\u003c/p>\n\u003cp>Talk to any wine lover in California and they'll tell you how lucky they are to live in such rich wine-producing region. Take the recent meeting of the San Francisco Wine Lovers Group at Toast wine bar in Oakland, where the favorites are California Pinot Noir, Russian River Zinfandel, and Napa Cabernet.\u003c/p>\n\u003cp>In fact, the type of grape – or varietal - is how most of us think about wine.\u003c/p>\n\u003cp>\"That's the big problem,\" says Andy Walker, a grape breeder in \u003ca href=\"http://wineserver.ucdavis.edu/\">Viticulture and Enology\u003c/a> at the University of California-Davis. \"We've spent the last 100 years emphasizing varieties and we've really marketed those names very effectively.\"\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Walker is strolling through UC Davis's test vineyard, where hundreds of different wine grapes from around the world are grown. The vast majority are unknown to consumers, because most wineries focus on only a handful of grapes. \"Chardonnay, cabernet, merlot, pinot noir – those would make up probably a large percentage,\" he says.\u003c/p>\n\u003cp>Those are all French varieties, mostly suited for cool climates. California is warm by comparison and thanks to climate change, it's expected to get a lot warmer. Extreme heat can be the enemy of good wine. \"It destroys acidity primarily and it changes color and aromatics,\" says Walker.\u003c/p>\n\u003cp>According to \u003ca href=\"http://news.stanford.edu/news/2011/june/wines-global-warming-063011.html\">a recent study\u003c/a> from Stanford University, about two degrees of warming could reduce California's premium wine-growing land by 30 to 50 percent. That could happen as soon as 2040. Water supply is also expected to be an issue.\u003c/p>\n\u003cp>\"I think the interesting thing for me as a breeder is to take advantage of this and say, OK, here's a chance now to change thought and let's actually readapt varieties to California,\" he says.\u003c/p>\n\u003cfigure id=\"attachment_22840\" class=\"wp-caption alignright\" style=\"max-width: 253px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/P1010793.jpg\">\u003cimg class=\"size-thumbnail wp-image-22840\" title=\"UC Davis \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/P1010793-253x169.jpg\" alt=\"\" width=\"253\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Andy Walker walks through UC Davis's test vineyard.\u003c/figcaption>\u003c/figure>\n\u003cp>But in many circles, grape breeding is a dirty term, according to Walker.\u003c/p>\n\u003cp>\"Viticulture is the most backward form of horticulture that exists. We use these varieties that haven't been changed for decades, for millennia in some cases. And it really doesn't make any sense.\"\u003c/p>\n\u003cp>The problem starts in today's vineyards. If you look at rows of Pinot Noir vines, you aren't just looking at the original varietal. You're looking at clones. That's because vines are grown from a branch that's taken off an existing plant.\u003c/p>\n\u003cp>\"Pinot noir is being propagated year after year after year. This essentially means that grapes have not been having sex very much,\" says Sean Myles , a geneticist at the Nova Scotia Agricultural College.\u003c/p>\n\u003cp>He says breeding is key for other crops, since farmers need seeds to plant every year. Wine grapes miss this opportunity to develop adaptability and disease resistance, since vines don't grow from seeds\u003c/p>\n\u003cp>\"That means that we're not allowing the genetic material to be shuffled anymore. That genetic material is now standing still in time. And while the pathogens are evolving, the pinot noir is not,\" says Myles.\u003c/p>\n\u003cp>Andy Walker says there's plenty of genetic diversity out there for breeding, if you wanted to make today's varieties more heat tolerant or drought resistant. But there's a very big problem. Once your breed your pinot noir with something else, you can't call it pinot noir anymore.\u003c/p>\n\u003cp>\"The last decision that hardest. Can we market this variety? We know it produces exceptional wine. We know the quality is better. But the next step is can we actually market it,\" says Walker.\u003c/p>\n\u003cp>That's a deal breaker for many vineyards, who think consumers won't buy varieties they don't recognize. Walker says looking ahead to climate change, there are already varieties out there today from Italy and Spain that would do well in a warmer California. \"We could produce Barbera instead, or Negroamaro or Nero d'Avola from southern Italy and we'd be far better ahead.\"\u003c/p>\n\u003cp>These lush reds are popular in Italy but not so well known to Californians. Walker says it'll come down to marketing. \"I don't think it's the consumer that's gonna make the shift. They have to be directed.\"\u003c/p>\n\u003cp>\"I think it's really a pull from consumers,\" says Nick Dokoozlian, a Vice President at \u003ca href=\"http://gallo.com/\">E & J Gallo Winery\u003c/a>, the largest family-owned winery in the US. \"In most cases, we're responding to consumer demand for a cultivar.\"\u003c/p>\n\u003cp>Dokoozlian says Gallo has been testing new wine varieties throughout its vineyards and has found some promising grapes. \"The problem is we can't necessarily sell those varieties. Consumers aren't aware of them. The marketing aspect of climate change and the adaptation to climate change, really, the hurdles on the marketing side are much, much more significant.\"\u003c/p>\n\u003cp>Since vineyards can last up to 30 years, he says switching varieties is a major financial gamble. \"The wine business is an extremely capital intensive business. The financial risk of planting the wrong variety in the wrong place is pretty significant.\"\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Still, given the temperature and water supply changes projected for California, Dokoozlian sees the market shifting eventually. \"I'm looking forward to having world-class California Nero d'Avola soon.\"\u003c/p>\n\n","blocks":[],"excerpt":"You’ve probably heard of the wines that made Napa and Sonoma famous, like Cabernet Sauvignon or Chardonnay. But what about Negroamaro or Nero d’Avola? They’re wine grapes that are well-adapted to hotter temperatures -- the kind of conditions that California may be facing as the climate continues to warm. ","status":"publish","parent":0,"modified":1450495858,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":25,"wordCount":934},"headData":{"title":"The Heat is On For California Wines | KQED","description":"","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"22785 http://science.kqed.org/quest/audio/heat-is-on-for-california-wines/","disqusUrl":"https://ww2.kqed.org/quest/2012/09/04/heat-is-on-for-california-wines/","disqusTitle":"The Heat is On For California Wines","source":"Climate","sourceUrl":"http://ww2.kqed.org/quest/category/climate/","audioUrl":"http://www.kqed.org/.stream/anon/radio/quest/2012/09/2012-09-03-quest.mp3","path":"/quest/22785/heat-is-on-for-california-wines","audioDuration":null,"audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>You've probably heard of the wines that made Napa and Sonoma famous, like Cabernet Sauvignon or Chardonnay. But what about \u003ca href=\"http://en.wikipedia.org/wiki/Negroamaro\">Negroamaro\u003c/a> or \u003ca href=\"http://en.wikipedia.org/wiki/Nero_d%27Avola\">Nero d'Avola\u003c/a>?\u003c/p>\n\u003cp>They're wine grapes that are well-adapted to hotter climates – the kind of conditions that California may be facing as the climate continues to warm. But for wineries that have staked their reputations on certain wines, adapting to climate change could be a tough sell.\u003c/p>\n\u003cp>Talk to any wine lover in California and they'll tell you how lucky they are to live in such rich wine-producing region. Take the recent meeting of the San Francisco Wine Lovers Group at Toast wine bar in Oakland, where the favorites are California Pinot Noir, Russian River Zinfandel, and Napa Cabernet.\u003c/p>\n\u003cp>In fact, the type of grape – or varietal - is how most of us think about wine.\u003c/p>\n\u003cp>\"That's the big problem,\" says Andy Walker, a grape breeder in \u003ca href=\"http://wineserver.ucdavis.edu/\">Viticulture and Enology\u003c/a> at the University of California-Davis. \"We've spent the last 100 years emphasizing varieties and we've really marketed those names very effectively.\"\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Walker is strolling through UC Davis's test vineyard, where hundreds of different wine grapes from around the world are grown. The vast majority are unknown to consumers, because most wineries focus on only a handful of grapes. \"Chardonnay, cabernet, merlot, pinot noir – those would make up probably a large percentage,\" he says.\u003c/p>\n\u003cp>Those are all French varieties, mostly suited for cool climates. California is warm by comparison and thanks to climate change, it's expected to get a lot warmer. Extreme heat can be the enemy of good wine. \"It destroys acidity primarily and it changes color and aromatics,\" says Walker.\u003c/p>\n\u003cp>According to \u003ca href=\"http://news.stanford.edu/news/2011/june/wines-global-warming-063011.html\">a recent study\u003c/a> from Stanford University, about two degrees of warming could reduce California's premium wine-growing land by 30 to 50 percent. That could happen as soon as 2040. Water supply is also expected to be an issue.\u003c/p>\n\u003cp>\"I think the interesting thing for me as a breeder is to take advantage of this and say, OK, here's a chance now to change thought and let's actually readapt varieties to California,\" he says.\u003c/p>\n\u003cfigure id=\"attachment_22840\" class=\"wp-caption alignright\" style=\"max-width: 253px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/P1010793.jpg\">\u003cimg class=\"size-thumbnail wp-image-22840\" title=\"UC Davis \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/P1010793-253x169.jpg\" alt=\"\" width=\"253\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Andy Walker walks through UC Davis's test vineyard.\u003c/figcaption>\u003c/figure>\n\u003cp>But in many circles, grape breeding is a dirty term, according to Walker.\u003c/p>\n\u003cp>\"Viticulture is the most backward form of horticulture that exists. We use these varieties that haven't been changed for decades, for millennia in some cases. And it really doesn't make any sense.\"\u003c/p>\n\u003cp>The problem starts in today's vineyards. If you look at rows of Pinot Noir vines, you aren't just looking at the original varietal. You're looking at clones. That's because vines are grown from a branch that's taken off an existing plant.\u003c/p>\n\u003cp>\"Pinot noir is being propagated year after year after year. This essentially means that grapes have not been having sex very much,\" says Sean Myles , a geneticist at the Nova Scotia Agricultural College.\u003c/p>\n\u003cp>He says breeding is key for other crops, since farmers need seeds to plant every year. Wine grapes miss this opportunity to develop adaptability and disease resistance, since vines don't grow from seeds\u003c/p>\n\u003cp>\"That means that we're not allowing the genetic material to be shuffled anymore. That genetic material is now standing still in time. And while the pathogens are evolving, the pinot noir is not,\" says Myles.\u003c/p>\n\u003cp>Andy Walker says there's plenty of genetic diversity out there for breeding, if you wanted to make today's varieties more heat tolerant or drought resistant. But there's a very big problem. Once your breed your pinot noir with something else, you can't call it pinot noir anymore.\u003c/p>\n\u003cp>\"The last decision that hardest. Can we market this variety? We know it produces exceptional wine. We know the quality is better. But the next step is can we actually market it,\" says Walker.\u003c/p>\n\u003cp>That's a deal breaker for many vineyards, who think consumers won't buy varieties they don't recognize. Walker says looking ahead to climate change, there are already varieties out there today from Italy and Spain that would do well in a warmer California. \"We could produce Barbera instead, or Negroamaro or Nero d'Avola from southern Italy and we'd be far better ahead.\"\u003c/p>\n\u003cp>These lush reds are popular in Italy but not so well known to Californians. Walker says it'll come down to marketing. \"I don't think it's the consumer that's gonna make the shift. They have to be directed.\"\u003c/p>\n\u003cp>\"I think it's really a pull from consumers,\" says Nick Dokoozlian, a Vice President at \u003ca href=\"http://gallo.com/\">E & J Gallo Winery\u003c/a>, the largest family-owned winery in the US. \"In most cases, we're responding to consumer demand for a cultivar.\"\u003c/p>\n\u003cp>Dokoozlian says Gallo has been testing new wine varieties throughout its vineyards and has found some promising grapes. \"The problem is we can't necessarily sell those varieties. Consumers aren't aware of them. The marketing aspect of climate change and the adaptation to climate change, really, the hurdles on the marketing side are much, much more significant.\"\u003c/p>\n\u003cp>Since vineyards can last up to 30 years, he says switching varieties is a major financial gamble. \"The wine business is an extremely capital intensive business. The financial risk of planting the wrong variety in the wrong place is pretty significant.\"\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Still, given the temperature and water supply changes projected for California, Dokoozlian sees the market shifting eventually. \"I'm looking forward to having world-class California Nero d'Avola soon.\"\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/22785/heat-is-on-for-california-wines","authors":["239"],"series":["quest_13295"],"categories":["quest_4","quest_6","quest_9"],"tags":["quest_252","quest_9990","quest_13195","quest_621","quest_1197","quest_9989","quest_1914","quest_13203","quest_9991","quest_2220","quest_13","quest_2727","quest_3022","quest_3171"],"collections":["quest_3354"],"featImg":"quest_22837","label":"source_quest_22785"},"quest_42743":{"type":"posts","id":"quest_42743","meta":{"index":"posts_1591205157","site":"quest","id":"42743","score":null,"sort":[1345475213000]},"guestAuthors":[],"slug":"arm-yourselves-for-the-upcoming-genetics-revolution","title":"Arm Yourselves for the Upcoming (Genetics) Revolution","publishDate":1345475213,"format":"standard","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_42745\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/stanfordatthetech/\" rel=\"attachment wp-att-42745\">\u003cimg class=\"size-full wp-image-42745\" title=\"StanfordAtTheTech\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/StanfordAtTheTech.jpg\" alt=\"\" width=\"640\" height=\"367\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/08/StanfordAtTheTech.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/StanfordAtTheTech-400x229.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">A multipronged approach to increasing genetics understanding.\u003c/figcaption>\u003c/figure>\n\u003cp>In the not too distant future, we’ll all have a map of our DNA in our hands. And lots of studies show that most of us are woefully unprepared for this latest genetic revolution. (See the links at the end for a selection of these studies.)\u003c/p>\n\u003cp>As a nation, we aren’t teaching the right genetics in our schools. And for those of us out of school, the situation is, if anything, even worse. By and large we lack the fundamental knowledge needed to properly interpret the avalanche of data headed our way.\u003c/p>\n\u003cp>Without this kind of knowledge, we are sure to get bamboozled by hucksters out there willing to sell us the “right” snake oil based on our DNA data. Even scarier, we may not make the right health decisions based on our DNA. And don’t necessarily count on your doctor for help navigating your way through these data. They are often as unprepared as the rest of us.\u003c/p>\n\u003cfigure id=\"attachment_42768\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/blaschkos_lines.jpg\">\u003cimg class=\"size-full wp-image-42768\" title=\"blaschkos_lines\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/blaschkos_lines.jpg\" alt=\"\" width=\"150\" height=\"200\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Chimeras are so cool! Sometimes these lines become apparent in chimeras under UV light.\u003c/figcaption>\u003c/figure>\n\u003cp>This is a big reason that the \u003ca href=\"http://genetics.stanford.edu/outreach/tech.html\">Stanford at The Tech program\u003c/a> has decided to publish the book, \u003cem>\u003ca href=\"http://genetics.thetech.org/book-titles\">When Will Broccoli Taste like Chocolate?\u003c/a>\u003c/em> (you can buy it from Amazon \u003ca href=\"http://www.amazon.com/gp/product/1477578714/ref=as_li_qf_sp_asin_il_tl?ie=UTF8&camp=1789&creative=9325&creativeASIN=1477578714&linkCode=as2&tag=staatthetec-20\">here\u003c/a>). It is a book that teaches genetics in a fun way by focusing on interesting cases and explaining the genetics behind them. Without even trying, you’ll get the solid footing you need to interpret your DNA. Or at the very least understand other people’s interpretations!\u003c/p>\n\u003cp>One of my favorite parts is the section on chimeras. Chimeras are fraternal twins who fused together at a very early stage of development. They are a single person who has one set of cells (and so one set of DNA) from one twin and another set of cells (and DNA) from the other twin.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>These chimeras don’t have two heads and four arms or anything like that. In fact, their differences are usually so subtle that they are invisible to the naked eye. They are often revealed only after they take some sort of genetic test (like a \u003ca href=\"http://www.mymultiplesclerosis.co.uk/misc/chimera.html\">paternity test\u003c/a> or a \u003ca href=\"http://www.katewerk.com/chimera.html\">tissue typing test\u003c/a> to find a new organ). And then what a revelation! Often the tests come back saying the chimera is not the parent of his or her children.\u003c/p>\n\u003cp>Chimeras are a great way to learn about DNA, genes, genetic tests and so on. And as you’ll see in the excerpt below, once you add in a link to a \u003ca href=\"http://www.csiguide.com/episodedetail.aspx?csi=157\">CSI episode\u003c/a> where a rapist almost gets away because he is a chimera, you end up with a fascinating read.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/excerpt500wwbtlc/\" rel=\"attachment wp-att-42744\">\u003cimg class=\"aligncenter size-full wp-image-42744\" title=\"Excerpt500WWBTLC\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Excerpt500WWBTLC.gif\" alt=\"\" width=\"500\" height=\"755\">\u003c/a>\u003c/p>\n\u003cp>The story goes on to explain why a chimera isn't torn apart by its immune system, other ways besides chimeras to have multiple DNAs and lots more.\u003c/p>\n\u003cp>For parents and parents-to-be, there is a section on eye and hair color so they can understand how their children ended up with the coloring they got. For example, blue-eyed parents can breathe a sigh of relief if they have a green or brown eyed child because we show that despite what your high school biology teacher told you, this can and does happen. Parents-to-be can even use this information to predict what hair and eye color their children are most likely to have!\u003c/p>\n\u003cfigure id=\"attachment_42769\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/browneye/\" rel=\"attachment wp-att-42769\">\u003cimg class=\"size-full wp-image-42769\" title=\"BrownEye\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/BrownEye.jpg\" alt=\"\" width=\"150\" height=\"150\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye.jpg 150w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-32x32.jpg 32w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-64x64.jpg 64w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-96x96.jpg 96w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-128x128.jpg 128w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-75x75.jpg 75w\" sizes=\"(max-width: 150px) 100vw, 150px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This person could have had blue eyed parents.\u003c/figcaption>\u003c/figure>\n\u003cp>For people who want to know how embryos from different species decide whether to be a boy or a girl, there is a great section on Nemo the clownfish. And there is a cool section on all the genetic information we can get from poop. And...\u003c/p>\n\u003cp>Add to this book our \u003ca href=\"http://genetics.stanford.edu/outreach/tech.html\">Stanford at The Tech\u003c/a> program that provides hands-on activities at \u003ca href=\"http://www.thetech.org/\">The Tech Museum\u003c/a> in San Jose (as well as at other venues) and our \u003ca href=\"http://genetics.thetech.org/\">Understanding Genetics\u003c/a> website, and you get a full frontal assault on the lack of genetics knowledge out there. We aim to demystify genetics and show how entertaining and interesting it really is. Perhaps a better title for the book might have been, \u003cem>When Will Genetics be like a Day at Disneyland?\u003c/em>. That day may be here sooner than you think.\u003c/p>\n\u003cp>For fun, here is a quick quiz I whipped up to test your genetics IQ. To make things interesting, the first person to get them all right gets a free copy of \u003cem>\u003ca href=\"http://genetics.thetech.org/book-titles\">When Will Broccoli Taste like Chocolate?\u003c/a>\u003c/em>. You can answer here, on \u003ca href=\"http://www.facebook.com/UnderstandGenetics\">Facebook\u003c/a> or, if you’re like me and you’d rather use email, send your answers to askageneticist@thetech.org. Good luck and enjoy!\u003c/p>\n\u003cp>1) Should you necessarily be scared if you find out you are 10 times more likely to get a rare cancer?\u003c/p>\n\u003cp>2) If you look like your mom, are you more likely to get the diseases that run in her family or your dad’s family?\u003c/p>\n\u003cp>3) If you have the recessive disease sickle cell anemia, should your kids be tested to see if they are carriers?\u003c/p>\n\u003cp>4) If you look like your dad, did you get more of his DNA?\u003c/p>\n\u003cp>5) If you flip a coin and get heads ten times in a row, what are the chances that the next flip will be a head?\u003c/p>\n\u003cp>6) True or false: Each cell in your body has the same DNA.\u003c/p>\n\u003cp>\u003cstrong>Studies cataloging the public’s lack of genetics knowledge:\u003c/strong>\u003cem>\u003cbr>\n\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/19039252\">\u003cbr>\nAustralian study on public knowledge of human genetics and health\u003c/a>.\u003cbr>\n\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/20512408\">\u003cbr>\nMisunderstandings concerning genetics among patients confronting genetic disease.\u003c/a>\u003c/em>\u003c/p>\n\u003cp>\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/18245328\">Essay contest reveals misconceptions of high school students in genetics content\u003c/a>.\u003c/p>\n\u003cp>\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/21885828\">A comprehensive analysis of high school genetics standards: are states keeping pace with modern genetics?\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>You can buy the book from Amazon \u003ca href=\"http://www.amazon.com/gp/product/1477578714/ref=as_li_qf_sp_asin_il_tl?ie=UTF8&camp=1789&creative=9325&creativeASIN=1477578714&linkCode=as2&tag=staatthetec-20\">here\u003c/a>.\u003c/p>\n\n","blocks":[],"excerpt":"As a nation, we aren’t teaching the right genetics in our schools. And for those of us out of school, the situation is, if anything, even worse. By and large we lack the fundamental knowledge needed to properly interpret the avalanche of data headed our way. ","status":"publish","parent":0,"modified":1346782049,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":25,"wordCount":971},"headData":{"title":"Arm Yourselves for the Upcoming (Genetics) Revolution | KQED","description":"As a nation, we aren’t teaching the right genetics in our schools. And for those of us out of school, the situation is, if anything, even worse. By and large we lack the fundamental knowledge needed to properly interpret the avalanche of data headed our way. ","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"42743 http://science.kqed.org/quest/?p=42743","disqusUrl":"https://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/","disqusTitle":"Arm Yourselves for the Upcoming (Genetics) Revolution","path":"/quest/42743/arm-yourselves-for-the-upcoming-genetics-revolution","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_42745\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/stanfordatthetech/\" rel=\"attachment wp-att-42745\">\u003cimg class=\"size-full wp-image-42745\" title=\"StanfordAtTheTech\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/StanfordAtTheTech.jpg\" alt=\"\" width=\"640\" height=\"367\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/08/StanfordAtTheTech.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/StanfordAtTheTech-400x229.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">A multipronged approach to increasing genetics understanding.\u003c/figcaption>\u003c/figure>\n\u003cp>In the not too distant future, we’ll all have a map of our DNA in our hands. And lots of studies show that most of us are woefully unprepared for this latest genetic revolution. (See the links at the end for a selection of these studies.)\u003c/p>\n\u003cp>As a nation, we aren’t teaching the right genetics in our schools. And for those of us out of school, the situation is, if anything, even worse. By and large we lack the fundamental knowledge needed to properly interpret the avalanche of data headed our way.\u003c/p>\n\u003cp>Without this kind of knowledge, we are sure to get bamboozled by hucksters out there willing to sell us the “right” snake oil based on our DNA data. Even scarier, we may not make the right health decisions based on our DNA. And don’t necessarily count on your doctor for help navigating your way through these data. They are often as unprepared as the rest of us.\u003c/p>\n\u003cfigure id=\"attachment_42768\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/blaschkos_lines.jpg\">\u003cimg class=\"size-full wp-image-42768\" title=\"blaschkos_lines\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/blaschkos_lines.jpg\" alt=\"\" width=\"150\" height=\"200\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Chimeras are so cool! Sometimes these lines become apparent in chimeras under UV light.\u003c/figcaption>\u003c/figure>\n\u003cp>This is a big reason that the \u003ca href=\"http://genetics.stanford.edu/outreach/tech.html\">Stanford at The Tech program\u003c/a> has decided to publish the book, \u003cem>\u003ca href=\"http://genetics.thetech.org/book-titles\">When Will Broccoli Taste like Chocolate?\u003c/a>\u003c/em> (you can buy it from Amazon \u003ca href=\"http://www.amazon.com/gp/product/1477578714/ref=as_li_qf_sp_asin_il_tl?ie=UTF8&camp=1789&creative=9325&creativeASIN=1477578714&linkCode=as2&tag=staatthetec-20\">here\u003c/a>). It is a book that teaches genetics in a fun way by focusing on interesting cases and explaining the genetics behind them. Without even trying, you’ll get the solid footing you need to interpret your DNA. Or at the very least understand other people’s interpretations!\u003c/p>\n\u003cp>One of my favorite parts is the section on chimeras. Chimeras are fraternal twins who fused together at a very early stage of development. They are a single person who has one set of cells (and so one set of DNA) from one twin and another set of cells (and DNA) from the other twin.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>These chimeras don’t have two heads and four arms or anything like that. In fact, their differences are usually so subtle that they are invisible to the naked eye. They are often revealed only after they take some sort of genetic test (like a \u003ca href=\"http://www.mymultiplesclerosis.co.uk/misc/chimera.html\">paternity test\u003c/a> or a \u003ca href=\"http://www.katewerk.com/chimera.html\">tissue typing test\u003c/a> to find a new organ). And then what a revelation! Often the tests come back saying the chimera is not the parent of his or her children.\u003c/p>\n\u003cp>Chimeras are a great way to learn about DNA, genes, genetic tests and so on. And as you’ll see in the excerpt below, once you add in a link to a \u003ca href=\"http://www.csiguide.com/episodedetail.aspx?csi=157\">CSI episode\u003c/a> where a rapist almost gets away because he is a chimera, you end up with a fascinating read.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/excerpt500wwbtlc/\" rel=\"attachment wp-att-42744\">\u003cimg class=\"aligncenter size-full wp-image-42744\" title=\"Excerpt500WWBTLC\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Excerpt500WWBTLC.gif\" alt=\"\" width=\"500\" height=\"755\">\u003c/a>\u003c/p>\n\u003cp>The story goes on to explain why a chimera isn't torn apart by its immune system, other ways besides chimeras to have multiple DNAs and lots more.\u003c/p>\n\u003cp>For parents and parents-to-be, there is a section on eye and hair color so they can understand how their children ended up with the coloring they got. For example, blue-eyed parents can breathe a sigh of relief if they have a green or brown eyed child because we show that despite what your high school biology teacher told you, this can and does happen. Parents-to-be can even use this information to predict what hair and eye color their children are most likely to have!\u003c/p>\n\u003cfigure id=\"attachment_42769\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/08/20/arm-yourselves-for-the-upcoming-genetics-revolution/browneye/\" rel=\"attachment wp-att-42769\">\u003cimg class=\"size-full wp-image-42769\" title=\"BrownEye\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/BrownEye.jpg\" alt=\"\" width=\"150\" height=\"150\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye.jpg 150w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-32x32.jpg 32w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-64x64.jpg 64w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-96x96.jpg 96w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-128x128.jpg 128w, https://ww2.kqed.org/app/uploads/sites/39/2012/08/BrownEye-75x75.jpg 75w\" sizes=\"(max-width: 150px) 100vw, 150px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This person could have had blue eyed parents.\u003c/figcaption>\u003c/figure>\n\u003cp>For people who want to know how embryos from different species decide whether to be a boy or a girl, there is a great section on Nemo the clownfish. And there is a cool section on all the genetic information we can get from poop. And...\u003c/p>\n\u003cp>Add to this book our \u003ca href=\"http://genetics.stanford.edu/outreach/tech.html\">Stanford at The Tech\u003c/a> program that provides hands-on activities at \u003ca href=\"http://www.thetech.org/\">The Tech Museum\u003c/a> in San Jose (as well as at other venues) and our \u003ca href=\"http://genetics.thetech.org/\">Understanding Genetics\u003c/a> website, and you get a full frontal assault on the lack of genetics knowledge out there. We aim to demystify genetics and show how entertaining and interesting it really is. Perhaps a better title for the book might have been, \u003cem>When Will Genetics be like a Day at Disneyland?\u003c/em>. That day may be here sooner than you think.\u003c/p>\n\u003cp>For fun, here is a quick quiz I whipped up to test your genetics IQ. To make things interesting, the first person to get them all right gets a free copy of \u003cem>\u003ca href=\"http://genetics.thetech.org/book-titles\">When Will Broccoli Taste like Chocolate?\u003c/a>\u003c/em>. You can answer here, on \u003ca href=\"http://www.facebook.com/UnderstandGenetics\">Facebook\u003c/a> or, if you’re like me and you’d rather use email, send your answers to askageneticist@thetech.org. Good luck and enjoy!\u003c/p>\n\u003cp>1) Should you necessarily be scared if you find out you are 10 times more likely to get a rare cancer?\u003c/p>\n\u003cp>2) If you look like your mom, are you more likely to get the diseases that run in her family or your dad’s family?\u003c/p>\n\u003cp>3) If you have the recessive disease sickle cell anemia, should your kids be tested to see if they are carriers?\u003c/p>\n\u003cp>4) If you look like your dad, did you get more of his DNA?\u003c/p>\n\u003cp>5) If you flip a coin and get heads ten times in a row, what are the chances that the next flip will be a head?\u003c/p>\n\u003cp>6) True or false: Each cell in your body has the same DNA.\u003c/p>\n\u003cp>\u003cstrong>Studies cataloging the public’s lack of genetics knowledge:\u003c/strong>\u003cem>\u003cbr>\n\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/19039252\">\u003cbr>\nAustralian study on public knowledge of human genetics and health\u003c/a>.\u003cbr>\n\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/20512408\">\u003cbr>\nMisunderstandings concerning genetics among patients confronting genetic disease.\u003c/a>\u003c/em>\u003c/p>\n\u003cp>\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/18245328\">Essay contest reveals misconceptions of high school students in genetics content\u003c/a>.\u003c/p>\n\u003cp>\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/21885828\">A comprehensive analysis of high school genetics standards: are states keeping pace with modern genetics?\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>You can buy the book from Amazon \u003ca href=\"http://www.amazon.com/gp/product/1477578714/ref=as_li_qf_sp_asin_il_tl?ie=UTF8&camp=1789&creative=9325&creativeASIN=1477578714&linkCode=as2&tag=staatthetec-20\">here\u003c/a>.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/42743/arm-yourselves-for-the-upcoming-genetics-revolution","authors":["6177"],"categories":["quest_4","quest_12"],"tags":["quest_3590","quest_1197","quest_11373","quest_3974","quest_13202","quest_2532","quest_3319"],"featImg":"quest_42745","label":"quest"},"quest_42806":{"type":"posts","id":"quest_42806","meta":{"index":"posts_1591205157","site":"quest","id":"42806","score":null,"sort":[1345240126000]},"guestAuthors":[],"slug":"building-a-better-tastier-tomato","title":"Building a Better, Tastier Tomato","publishDate":1345240126,"format":"audio","headTitle":"QUEST | KQED Science","labelTerm":{},"content":"\u003cp>Decades ago, researchers figured out how to create the picture-perfect tomato that travels well and is available year-round. The trouble is, as any supermarket shopper can tell you, tomatoes that look great sometimes taste terrible.\u003c/p>\n\u003cp>It’s not hard to see how much some tomatoes have changed. Just take the trucks on California highways during the summer, each pulling a double trailer stacked high with tomatoes. There’s a reason the tomatoes at the bottom of the pile aren’t squished into a tomato-y mess. That's thanks to the \u003ca href=\"http://daviswiki.org/square_tomato\">square tomato\u003c/a>.\u003c/p>\n\u003cp>“The square tomato is kind of a misnomer,” says Roger Chetelat, director of the Tomato Genetics Resource Center at the University of California-Davis. We’re in a greenhouse on campus where he’s holding a few square tomatoes.\u003c/p>\n\u003cp>“You can see they’re not square but they are blocky,” he says. The tomatoes are sort of flat on the side and are firm to the touch even though they’re ripe, sort of like a baseball. “I think I’d prefer to have a tomato like that thrown at me than a baseball, but yeah, they’re pretty tough,” Chetelat says.\u003c/p>\n\u003cp>Fifty years ago, farmers were looking for tougher tomatoes that could withstand new mechanical picking machines. So, plant breeders at UC Davis created a tomato with thick skin and a firm, meaty inside. California’s tomato production boomed.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>Unintended Genetic Consequences\u003c/strong>\u003c/p>\n\u003cp>But the era of modern plant breeding came with some unintended effects, as UC Davis researcher Ann Powell discovered.\u003c/p>\n\u003cp>She demonstrates with a genetic taste test, of sorts. “We can try one of these,” she says, cutting up a standard grocery store tomato. “Tastes tomato-y.”\u003c/p>\n\u003cfigure id=\"attachment_42812\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/GreenShoulders.jpg\">\u003cimg class=\"size-full wp-image-42812\" title=\"SONY DSC\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/GreenShoulders.jpg\" alt=\"\" width=\"300\" height=\"197\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Young tomatoes with green shoulders on the left and no shoulders on the right.\u003c/figcaption>\u003c/figure>\n\u003cp>The other one we’re sampling has what Powell calls “green shoulders.” That means, as it grew, the tomato was dark green on top around the stem – something that’s controlled by a specific gene.\u003c/p>\n\u003cp>“They’re sweeter,” Powell says, tasting it. “Whether it’s all due to that particular gene, I can’t tell you. But, I don’t know, you can taste the difference.”\u003c/p>\n\u003cp>If green shoulders don’t sound familiar, that’s because most commercial tomatoes don’t have them anymore. Seventy years ago, breeders selected for uniformly light green tomatoes with no shoulders, which stood out better against the plant’s dark leaves.\u003c/p>\n\u003cp>“They’re a lot easier to see so a farmer could judge his yield. They could see how productive the plants were a lot easier,” says Powell. Their uniform color was also more attractive to consumers.\u003c/p>\n\u003cp>It turns out, those green shoulders have a key job. “We found that it influences the amount of sugar in the ripe fruit,” she says. The dark green parts have more chloroplasts, which turn sunlight into sugars.\u003c/p>\n\u003cp>“It made about a 20 percent difference in the amount of sugars. I think of it a little bit like how you eat berries. Most of us, including me, sprinkle a little bit of sugar on top to sort of enhance the flavor,” says Powell.\u003c/p>\n\u003cfigure id=\"attachment_42819\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Powell.jpg\">\u003cimg class=\"size-full wp-image-42819\" title=\"Powell\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Powell.jpg\" alt=\"\" width=\"300\" height=\"212\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Ann Powell looks at tomatoes in a UC Davis greenhouse.\u003c/figcaption>\u003c/figure>\n\u003cp>Most heirloom tomatoes still have green shoulders, but Powell says now that they know about this gene, plant breeders could put it back in commercial varieties. And since the tomato genome was sequenced earlier this year, there are still other flavor genes to study.\u003c/p>\n\u003cp>\u003cstrong>Focusing on Taste and Nutrition\u003c/strong>\u003c/p>\n\u003cp>“We’ve modified and changed our food radically,” says Alyson Mitchell, professor in UC Davis’s Food Science and Technology Department.\u003c/p>\n\u003cp>“We’ve bred these seeds and plants to have all of these other characteristics: uniform shape, size, color, good disease resistance, high yield,” she says. That’s had major benefits: produce is widely available and more affordable.\u003c/p>\n\u003cp>On the other hand, “we’ve absolutely not paid attention to flavor and nutrition. You know, we’re telling children, eat more fruits and vegetables at a time that fruits and vegetables have never tasted worse,” Mitchell says.\u003c/p>\n\u003cp>Scientists are just starting to understand the molecular compounds that control taste and nutrition. “What we do know is that not all tomatoes are the same. Different cultivars have different levels of nutrients in them,” she says.\u003c/p>\n\u003cp>Growing them organically can also change the levels of nutrients. In a ten-year controlled study of tomatoes, organic tomatoes showed higher levels of antioxidants and molecules that make up flavor and color. But researchers still aren’t sure which of these compounds are the most important for our health. Take flavonoids, which have gotten a lot of hype as antioxidants.\u003c/p>\n\u003cp>“There are about sixteen hundred described flavonoids to date and we don’t even really at this point understand what that complement is, let alone what all of those different compounds do to benefit our health,” Mitchell says.\u003c/p>\n\u003cp>Even if there is one nutrient that stands out, it’s not always easy to enhance it. Take the case of “super broccoli.” “So they made this broccoli and the idea was to market it as a super broccoli because it had very high levels of this antioxidant, quercetin. Well quercetin is really bitter and they sat a bunch of people down to eat and nobody could eat it, it was so awful,” says Mitchell.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Mitchell says it’s probably the combination of nutrients that gives produce its punch, which they’re working to understand better. Until then, she says, there is one way to make sure you’re getting those benefits: follow your mom’s advice and eat more fruits and vegetables.\u003c/p>\n\n","blocks":[],"excerpt":"Many tomatoes have been bred to travel well and look appealing, but now researchers are focusing on making them more nutritious and better tasting.","status":"publish","parent":0,"modified":1450496230,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":26,"wordCount":1010},"headData":{"title":"Building a Better, Tastier Tomato | KQED","description":"Many tomatoes have been bred to travel well and look appealing, but now researchers are focusing on making them more nutritious and better tasting.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"42806 http://science.kqed.org/quest/?post_type=audio_reports&p=42806","disqusUrl":"https://ww2.kqed.org/quest/2012/08/17/building-a-better-tastier-tomato/","disqusTitle":"Building a Better, Tastier Tomato","source":"Food","sourceUrl":"http://ww2.kqed.org/quest/category/food/","audioUrl":"http://www.kqed.org/.stream/anon/radio/quest/2012/08/2012-08-20-quest.mp3","path":"/quest/42806/building-a-better-tastier-tomato","audioDuration":null,"audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>Decades ago, researchers figured out how to create the picture-perfect tomato that travels well and is available year-round. The trouble is, as any supermarket shopper can tell you, tomatoes that look great sometimes taste terrible.\u003c/p>\n\u003cp>It’s not hard to see how much some tomatoes have changed. Just take the trucks on California highways during the summer, each pulling a double trailer stacked high with tomatoes. There’s a reason the tomatoes at the bottom of the pile aren’t squished into a tomato-y mess. That's thanks to the \u003ca href=\"http://daviswiki.org/square_tomato\">square tomato\u003c/a>.\u003c/p>\n\u003cp>“The square tomato is kind of a misnomer,” says Roger Chetelat, director of the Tomato Genetics Resource Center at the University of California-Davis. We’re in a greenhouse on campus where he’s holding a few square tomatoes.\u003c/p>\n\u003cp>“You can see they’re not square but they are blocky,” he says. The tomatoes are sort of flat on the side and are firm to the touch even though they’re ripe, sort of like a baseball. “I think I’d prefer to have a tomato like that thrown at me than a baseball, but yeah, they’re pretty tough,” Chetelat says.\u003c/p>\n\u003cp>Fifty years ago, farmers were looking for tougher tomatoes that could withstand new mechanical picking machines. So, plant breeders at UC Davis created a tomato with thick skin and a firm, meaty inside. California’s tomato production boomed.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>Unintended Genetic Consequences\u003c/strong>\u003c/p>\n\u003cp>But the era of modern plant breeding came with some unintended effects, as UC Davis researcher Ann Powell discovered.\u003c/p>\n\u003cp>She demonstrates with a genetic taste test, of sorts. “We can try one of these,” she says, cutting up a standard grocery store tomato. “Tastes tomato-y.”\u003c/p>\n\u003cfigure id=\"attachment_42812\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/GreenShoulders.jpg\">\u003cimg class=\"size-full wp-image-42812\" title=\"SONY DSC\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/GreenShoulders.jpg\" alt=\"\" width=\"300\" height=\"197\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Young tomatoes with green shoulders on the left and no shoulders on the right.\u003c/figcaption>\u003c/figure>\n\u003cp>The other one we’re sampling has what Powell calls “green shoulders.” That means, as it grew, the tomato was dark green on top around the stem – something that’s controlled by a specific gene.\u003c/p>\n\u003cp>“They’re sweeter,” Powell says, tasting it. “Whether it’s all due to that particular gene, I can’t tell you. But, I don’t know, you can taste the difference.”\u003c/p>\n\u003cp>If green shoulders don’t sound familiar, that’s because most commercial tomatoes don’t have them anymore. Seventy years ago, breeders selected for uniformly light green tomatoes with no shoulders, which stood out better against the plant’s dark leaves.\u003c/p>\n\u003cp>“They’re a lot easier to see so a farmer could judge his yield. They could see how productive the plants were a lot easier,” says Powell. Their uniform color was also more attractive to consumers.\u003c/p>\n\u003cp>It turns out, those green shoulders have a key job. “We found that it influences the amount of sugar in the ripe fruit,” she says. The dark green parts have more chloroplasts, which turn sunlight into sugars.\u003c/p>\n\u003cp>“It made about a 20 percent difference in the amount of sugars. I think of it a little bit like how you eat berries. Most of us, including me, sprinkle a little bit of sugar on top to sort of enhance the flavor,” says Powell.\u003c/p>\n\u003cfigure id=\"attachment_42819\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Powell.jpg\">\u003cimg class=\"size-full wp-image-42819\" title=\"Powell\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/08/Powell.jpg\" alt=\"\" width=\"300\" height=\"212\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Ann Powell looks at tomatoes in a UC Davis greenhouse.\u003c/figcaption>\u003c/figure>\n\u003cp>Most heirloom tomatoes still have green shoulders, but Powell says now that they know about this gene, plant breeders could put it back in commercial varieties. And since the tomato genome was sequenced earlier this year, there are still other flavor genes to study.\u003c/p>\n\u003cp>\u003cstrong>Focusing on Taste and Nutrition\u003c/strong>\u003c/p>\n\u003cp>“We’ve modified and changed our food radically,” says Alyson Mitchell, professor in UC Davis’s Food Science and Technology Department.\u003c/p>\n\u003cp>“We’ve bred these seeds and plants to have all of these other characteristics: uniform shape, size, color, good disease resistance, high yield,” she says. That’s had major benefits: produce is widely available and more affordable.\u003c/p>\n\u003cp>On the other hand, “we’ve absolutely not paid attention to flavor and nutrition. You know, we’re telling children, eat more fruits and vegetables at a time that fruits and vegetables have never tasted worse,” Mitchell says.\u003c/p>\n\u003cp>Scientists are just starting to understand the molecular compounds that control taste and nutrition. “What we do know is that not all tomatoes are the same. Different cultivars have different levels of nutrients in them,” she says.\u003c/p>\n\u003cp>Growing them organically can also change the levels of nutrients. In a ten-year controlled study of tomatoes, organic tomatoes showed higher levels of antioxidants and molecules that make up flavor and color. But researchers still aren’t sure which of these compounds are the most important for our health. Take flavonoids, which have gotten a lot of hype as antioxidants.\u003c/p>\n\u003cp>“There are about sixteen hundred described flavonoids to date and we don’t even really at this point understand what that complement is, let alone what all of those different compounds do to benefit our health,” Mitchell says.\u003c/p>\n\u003cp>Even if there is one nutrient that stands out, it’s not always easy to enhance it. Take the case of “super broccoli.” “So they made this broccoli and the idea was to market it as a super broccoli because it had very high levels of this antioxidant, quercetin. Well quercetin is really bitter and they sat a bunch of people down to eat and nobody could eat it, it was so awful,” says Mitchell.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Mitchell says it’s probably the combination of nutrients that gives produce its punch, which they’re working to understand better. Until then, she says, there is one way to make sure you’re getting those benefits: follow your mom’s advice and eat more fruits and vegetables.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/42806/building-a-better-tastier-tomato","authors":["239"],"categories":["quest_4","quest_5","quest_9","quest_3229","quest_17"],"tags":["quest_252","quest_733","quest_1122","quest_1197","quest_10106","quest_13203","quest_2088","quest_10926","quest_2220","quest_3716","quest_13","quest_13364","quest_11374","quest_3022"],"featImg":"quest_42808","label":"source_quest_42806"},"quest_41121":{"type":"posts","id":"quest_41121","meta":{"index":"posts_1591205157","site":"quest","id":"41121","score":null,"sort":[1343055649000]},"guestAuthors":[],"slug":"pregnant-women-face-big-questions-with-cheaper-dna-sequencing","title":"Pregnant Women Face Big Questions With Cheaper DNA Sequencing","publishDate":1343055649,"format":"standard","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_41122\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/07/23/pregnant-women-face-big-questions-with-cheaper-dna-sequencing/9wkfetus/\" rel=\"attachment wp-att-41122\">\u003cimg class=\"size-full wp-image-41122\" title=\"9wkFetus\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/07/9wkFetus.jpg\" alt=\"\" width=\"640\" height=\"367\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/07/9wkFetus.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/07/9wkFetus-400x229.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Cheap DNA sequncing has the potential to help more children overcome genetic disease.\u003c/figcaption>\u003c/figure>\n\u003cp>In the very near future, a pregnant woman will be able to learn a whole lot more than she currently can about the fetus she is carrying. And she can find out in a way that poses no risk to the fetus.\u003c/p>\n\u003cp>This is obviously a good thing for fetuses with previously hidden but treatable genetic diseases and for parents of special needs children so they can prepare themselves. But it will also open wider the Pandora’s Box of ethical dilemmas that prenatal testing already presents us with.\u003c/p>\n\u003cp>The most common ways to do prenatal testing right now -- amniocentesis and chorionic villus sampling (CVS) -- increases a woman's risk for miscarriage. Not a lot, but enough so that the testing shouldn't routinely be done. Basically the only time to do this kind of testing is when the risk for the fetus having a genetic problem is higher than the risk of miscarriage.\u003c/p>\n\u003cp>This is why, for example, only fetuses of older women are routinely tested for Down syndrome. Once a woman turns 35 or so, the risk for having a child with Down syndrome is higher than the risk for miscarriage.\u003c/p>\n\u003cp>New technologies are changing this calculation so that in the near future, prenatal testing may be available for any woman who can afford it. Like I said, this holds great promise for helping parents and their children. But it also raises troubling questions about what parents might do with this information.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>The new technique is so much safer because unlike amniocentesis or CVS, it doesn’t mess with the fetus at all. All that is required is a blood draw from the mother. This is because a significant fraction of cell-free DNA in maternal blood comes from the fetus and because of how powerful and how cheap DNA sequencing has become.\u003c/p>\n\u003cp>Back \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/18838674\">in 2008\u003c/a>, DNA sequencing was powerful enough to use this technique to determine whether a fetus had extra or missing chromosomes. In other words, it could be used to figure out whether the fetus had Down syndrome (an extra chromosome 21), Turner syndrome (a single X with no Y), Edwards syndrome (an extra chromosome 18) and so on. These kinds of tests are being refined and will soon be widely available.\u003c/p>\n\u003cp>The test is actually a pretty simple one. Scientists do lots of DNA sequencing so they get a large number of different reads from each chromosome. They then compare the numbers and look for anything out of the ordinary.\u003c/p>\n\u003cp>This is easy to understand if you were just looking at the fetal DNA. In Down syndrome, you have three copies of chromosome 21 instead of the usual two. If you did this kind of sequencing, you’d find 1.5 times the usual amount of chromosome 21 DNA. So if all the other chromosomes gave 100 reads, a fetus with Down syndrome would give 150 for chromosome 21.\u003c/p>\n\u003cp>The cell-free DNA gives similar but much less pronounced results. Let’s say that the fetal DNA makes up about 19% of the total of cell-free DNA (this is a pretty typical number). When scientists compare all of the chromosomes, they will find an increased amount of chromosome 21 DNA but not as much as if they were looking just at fetal DNA. If I am doing my math right, they would get around 110 instead of 100 reads for chromosome 21. With enough DNA sequencing, this is enough to tell that the fetus has an extra chromosome 21.\u003c/p>\n\u003cfigure id=\"attachment_41127\" class=\"wp-caption aligncenter\" style=\"max-width: 400px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/07/23/pregnant-women-face-big-questions-with-cheaper-dna-sequencing/downresults/\" rel=\"attachment wp-att-41127\">\u003cimg class=\"size-full wp-image-41127\" title=\"DownResults\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/07/DownResults.jpg\" alt=\"\" width=\"400\" height=\"126\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The extra chromosome 21 DNA found in the cell free DNA of the mother\u003c/figcaption>\u003c/figure>\n\u003cp>Now DNA sequencing has become so cheap and powerful that scientists can use the same technique to get much more information about the fetus. Instead of looking at big changes like extra or missing chromosomes, they can actually look for lots and lots of specific DNA differences that can lead to disease. And even more astonishingly, the scientists in \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/22763444\">this report\u003c/a> were able to read all of a fetus’ genes base by base. They can now get a complete genetic readout of the fetus.\u003c/p>\n\u003cp>Reading every letter of every gene won’t be ready for primetime in the near future but being able to look for lots of different genetic markers will. And remember, this is all without any risk to the fetus. At least not from the procedure…\u003c/p>\n\u003cp>This technique will allow doctors to diagnose and treat more genetic diseases earlier than ever before which will be of great benefit for some patients. For example, there are some genetic diseases whose symptoms can be completely headed off if the disease is treated early enough with dietary changes. This test will be able to help some of these people for the first time.\u003c/p>\n\u003cp>But this kind of information is a double-edged sword. I have to wonder how parents-to-be might use it. There are already girl shortages in parts of India and China because of the selective abortion of females. And we know that \u003ca href=\"http://blogs.discovermagazine.com/gnxp/2008/09/down-syndrome-and-abortion-rates/\">90% or so \u003c/a>of confirmed Down syndrome pregnancies end in abortion. This new test will certainly increase the number of Down syndrome abortions because so many more women will be able to find out if their fetus has an extra chromosome 21 or not.\u003c/p>\n\u003cp>It is obviously wrong to terminate a pregnancy because the fetus has two X chromosomes. And many people are troubled by terminating Down syndrome pregnancies as the condition is not fatal and many people with Down syndrome can lead happy and productive lives.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>The question is, when parents-to-be can learn even more about their fetuses, what will be the result? What if the fetus is at increased risk for getting Alzheimer’s late in life? Or having high cholesterol? Or not having blue eyes?\u003c/p>\n\n","blocks":[],"excerpt":"In the very near future, a pregnant woman will be able to learn a whole lot more than she currently can about the fetus she is carrying. And she can find out in a way that poses no risk to the fetus.","status":"publish","parent":0,"modified":1344279299,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":18,"wordCount":989},"headData":{"title":"Pregnant Women Face Big Questions With Cheaper DNA Sequencing | KQED","description":"In the very near future, a pregnant woman will be able to learn a whole lot more than she currently can about the fetus she is carrying. And she can find out in a way that poses no risk to the fetus.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"41121 http://science.kqed.org/quest/?p=41121","disqusUrl":"https://ww2.kqed.org/quest/2012/07/23/pregnant-women-face-big-questions-with-cheaper-dna-sequencing/","disqusTitle":"Pregnant Women Face Big Questions With Cheaper DNA Sequencing","path":"/quest/41121/pregnant-women-face-big-questions-with-cheaper-dna-sequencing","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_41122\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/07/23/pregnant-women-face-big-questions-with-cheaper-dna-sequencing/9wkfetus/\" rel=\"attachment wp-att-41122\">\u003cimg class=\"size-full wp-image-41122\" title=\"9wkFetus\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/07/9wkFetus.jpg\" alt=\"\" width=\"640\" height=\"367\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/07/9wkFetus.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/07/9wkFetus-400x229.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Cheap DNA sequncing has the potential to help more children overcome genetic disease.\u003c/figcaption>\u003c/figure>\n\u003cp>In the very near future, a pregnant woman will be able to learn a whole lot more than she currently can about the fetus she is carrying. And she can find out in a way that poses no risk to the fetus.\u003c/p>\n\u003cp>This is obviously a good thing for fetuses with previously hidden but treatable genetic diseases and for parents of special needs children so they can prepare themselves. But it will also open wider the Pandora’s Box of ethical dilemmas that prenatal testing already presents us with.\u003c/p>\n\u003cp>The most common ways to do prenatal testing right now -- amniocentesis and chorionic villus sampling (CVS) -- increases a woman's risk for miscarriage. Not a lot, but enough so that the testing shouldn't routinely be done. Basically the only time to do this kind of testing is when the risk for the fetus having a genetic problem is higher than the risk of miscarriage.\u003c/p>\n\u003cp>This is why, for example, only fetuses of older women are routinely tested for Down syndrome. Once a woman turns 35 or so, the risk for having a child with Down syndrome is higher than the risk for miscarriage.\u003c/p>\n\u003cp>New technologies are changing this calculation so that in the near future, prenatal testing may be available for any woman who can afford it. Like I said, this holds great promise for helping parents and their children. But it also raises troubling questions about what parents might do with this information.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>The new technique is so much safer because unlike amniocentesis or CVS, it doesn’t mess with the fetus at all. All that is required is a blood draw from the mother. This is because a significant fraction of cell-free DNA in maternal blood comes from the fetus and because of how powerful and how cheap DNA sequencing has become.\u003c/p>\n\u003cp>Back \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/18838674\">in 2008\u003c/a>, DNA sequencing was powerful enough to use this technique to determine whether a fetus had extra or missing chromosomes. In other words, it could be used to figure out whether the fetus had Down syndrome (an extra chromosome 21), Turner syndrome (a single X with no Y), Edwards syndrome (an extra chromosome 18) and so on. These kinds of tests are being refined and will soon be widely available.\u003c/p>\n\u003cp>The test is actually a pretty simple one. Scientists do lots of DNA sequencing so they get a large number of different reads from each chromosome. They then compare the numbers and look for anything out of the ordinary.\u003c/p>\n\u003cp>This is easy to understand if you were just looking at the fetal DNA. In Down syndrome, you have three copies of chromosome 21 instead of the usual two. If you did this kind of sequencing, you’d find 1.5 times the usual amount of chromosome 21 DNA. So if all the other chromosomes gave 100 reads, a fetus with Down syndrome would give 150 for chromosome 21.\u003c/p>\n\u003cp>The cell-free DNA gives similar but much less pronounced results. Let’s say that the fetal DNA makes up about 19% of the total of cell-free DNA (this is a pretty typical number). When scientists compare all of the chromosomes, they will find an increased amount of chromosome 21 DNA but not as much as if they were looking just at fetal DNA. If I am doing my math right, they would get around 110 instead of 100 reads for chromosome 21. With enough DNA sequencing, this is enough to tell that the fetus has an extra chromosome 21.\u003c/p>\n\u003cfigure id=\"attachment_41127\" class=\"wp-caption aligncenter\" style=\"max-width: 400px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/07/23/pregnant-women-face-big-questions-with-cheaper-dna-sequencing/downresults/\" rel=\"attachment wp-att-41127\">\u003cimg class=\"size-full wp-image-41127\" title=\"DownResults\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/07/DownResults.jpg\" alt=\"\" width=\"400\" height=\"126\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The extra chromosome 21 DNA found in the cell free DNA of the mother\u003c/figcaption>\u003c/figure>\n\u003cp>Now DNA sequencing has become so cheap and powerful that scientists can use the same technique to get much more information about the fetus. Instead of looking at big changes like extra or missing chromosomes, they can actually look for lots and lots of specific DNA differences that can lead to disease. And even more astonishingly, the scientists in \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/22763444\">this report\u003c/a> were able to read all of a fetus’ genes base by base. They can now get a complete genetic readout of the fetus.\u003c/p>\n\u003cp>Reading every letter of every gene won’t be ready for primetime in the near future but being able to look for lots of different genetic markers will. And remember, this is all without any risk to the fetus. At least not from the procedure…\u003c/p>\n\u003cp>This technique will allow doctors to diagnose and treat more genetic diseases earlier than ever before which will be of great benefit for some patients. For example, there are some genetic diseases whose symptoms can be completely headed off if the disease is treated early enough with dietary changes. This test will be able to help some of these people for the first time.\u003c/p>\n\u003cp>But this kind of information is a double-edged sword. I have to wonder how parents-to-be might use it. There are already girl shortages in parts of India and China because of the selective abortion of females. And we know that \u003ca href=\"http://blogs.discovermagazine.com/gnxp/2008/09/down-syndrome-and-abortion-rates/\">90% or so \u003c/a>of confirmed Down syndrome pregnancies end in abortion. This new test will certainly increase the number of Down syndrome abortions because so many more women will be able to find out if their fetus has an extra chromosome 21 or not.\u003c/p>\n\u003cp>It is obviously wrong to terminate a pregnancy because the fetus has two X chromosomes. And many people are troubled by terminating Down syndrome pregnancies as the condition is not fatal and many people with Down syndrome can lead happy and productive lives.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>The question is, when parents-to-be can learn even more about their fetuses, what will be the result? What if the fetus is at increased risk for getting Alzheimer’s late in life? Or having high cholesterol? Or not having blue eyes?\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/41121/pregnant-women-face-big-questions-with-cheaper-dna-sequencing","authors":["6177"],"categories":["quest_4","quest_12"],"tags":["quest_3961","quest_868","quest_1197","quest_11303","quest_13202","quest_3319"],"featImg":"quest_41122","label":"quest"},"quest_39182":{"type":"posts","id":"quest_39182","meta":{"index":"posts_1591205157","site":"quest","id":"39182","score":null,"sort":[1339426811000]},"guestAuthors":[],"slug":"tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time","title":"Tackling the Cause of Cystic Fibrosis One Mutation at a Time","publishDate":1339426811,"format":"standard","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_39185\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/ivacaftor/\" rel=\"attachment wp-att-39185\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/06/Ivacaftor.jpg\" alt=\"\" title=\"Ivacaftor\" width=\"640\" height=\"365\" class=\"size-full wp-image-39185\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/06/Ivacaftor.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/06/Ivacaftor-400x228.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This little molecule is changing how some cystic fibrosis patients are treated. And how new drugs may be made in the future.\u003c/figcaption>\u003c/figure>\n\u003cp>There was big news in the cystic fibrosis (CF) field recently: a new CF drug called ivacaftor (or VX-770 or Kalydeco) has been approved that does more than target the symptoms of CF. It actually works to get the broken gene working again. \u003c/p>\n\u003cp>The good news is that this is the first treatment that has the potential to cure this genetic disease (as long as the patients keep taking their medicine). The bad news is that it is only approved for around 4-5% of people with CF. This last bit of news may get a lot better in the near future but ivacaftor will never help every CF sufferer.\u003c/p>\n\u003cp>The reason for this has to do with the fact that there is more than one way to break the main gene involved in CF -- the CFTR gene -- and that there is more than one class of CFTR break.\u003c/p>\n\u003cp>The CFTR gene has the instructions for making the CFTR protein. This protein needs to get made and sent to the membrane so it can do its job of shuttling chloride ions back and forth. If you have a slight difference* in the gene that disrupts any step, then you can end up with CF. (Although not every slight difference leads to CF -- not by a long shot!)\u003c/p>\n\u003cfigure id=\"attachment_39190\" class=\"wp-caption alignright\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/cftr/\" rel=\"attachment wp-att-39190\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/06/CFTR.jpg\" alt=\"\" title=\"CFTR\" width=\"250\" height=\"230\" class=\"size-full wp-image-39190\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">There are many ways to keep this protein from working. Each way may need a different medicine.\u003c/figcaption>\u003c/figure>\n\u003cp>So some CF-causing differences in the CFTR gene will keep the protein from being made while others will keep it from making it to the membrane. Still others will keep the channel from opening wide enough to let the chloride ions pass through. Ivacaftor helps people in this last category.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>These folks have a mutation in their gene called G551D. As you might recall, genes are written in a simple language that just has four letters—A, G, C, and T. These letters are all grouped together in a gene to form three letter words. \u003c/p>\n\u003cp>With the exception of three words that act like a period at the end of a sentence, each of these words corresponds to one of twenty different amino acids. So a gene is really just the instructions for stringing together certain amino acids in a certain order.\u003c/p>\n\u003cp>The CFTR protein is made up of 1470 of these three letter words. The people helped by ivacaftor have a letter change that causes the cell to read the 551st word as a D instead of a G. This is enough to cause the protein to have trouble letting the chloride ions through.\u003c/p>\n\u003cp>Ivacaftor enhances CFTR’s ability to open up. So it makes sense that it would help people with the G551D variation. But it also makes sense why it won’t help for other CF patients.\u003c/p>\n\u003cp>For example, around 10% of people with CF have what is called a nonsense mutation in their CFTR gene. What happens in these cases is that a word that normally corresponds to an amino acid is mutated so that it now codes for a period. The cell stops reading the gene too soon and so you end up with only a part of the protein. Usually these “truncated” proteins can’t do much of anything. \u003c/p>\n\u003cp>Giving one of these patients a drug that helps the full length protein open wider isn’t going to be of much help. No, you need a drug that will ignore the period and make at least some functional CFTR. And there is a drug in the pipeline called PTC-124 that just might be able to pull this off. Of course PTC-124 will be of little use for people with the G551D variant!\u003c/p>\n\u003cp>Now having said this, ivacaftor may be more than a one trick pony. In fact, it may be able to help the majority of people with CF in the near future. \u003c/p>\n\u003cfigure id=\"attachment_39195\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/atcgpeople/\" rel=\"attachment wp-att-39195\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/06/atcgPeople.jpg\" alt=\"\" title=\"atcgPeople\" width=\"150\" height=\"184\" class=\"size-full wp-image-39195\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Our genetic uniqueness will make finding cures more difficult.\u003c/figcaption>\u003c/figure>\n\u003cp>Most people with CF have a certain mutation called delta508. Basically the 508th word has gone missing in their CFTR gene.\u003c/p>\n\u003cp>What happens in these cases is that most of the CFTR protein gets lost on its way to the membrane. But a tiny bit does make it to the right place and ivacaftor might be able to boost that little bit enough to help these patients. \u003c/p>\n\u003cp>Ivacaftor is currently in Phase 2 clinical trials to see if it can help patients with the delta508 variant. The results are promising so far.\u003c/p>\n\u003cp>These treatments for CF are showing how we may have to deal with genetic diseases in the future. As I talked about in my last \u003ca href=\"http://ww2.kqed.org/quest/2012/05/28/why-your-newfound-uniqueness-a-nightmare-for-your-doctor/\">blog\u003c/a>, we are all unique genetically. This means that even simple genetic diseases are going to be like CF and come in many different classes that will all have to be treated differently. It also means that new drugs may only help a relatively small number of patients.\u003c/p>\n\u003cp>This last point will require a paradigm shift in how drugs are developed too. Most big pharma companies won’t touch drugs that treat so few people. Ivacaftor is showing us the way here too.\u003c/p>\n\u003cp>The Cystic Fibrosis Foundation provided big pharma with a sizeable chunk of change to get this drug through clinical trials and to the market. The new paradigm may be that interested patient groups collaborate with big pharma to get these “boutique” drugs to market. \u003c/p>\n\u003cp>It’ll be interesting to see if this is a viable business model. But at least for now a minority of CF patients can have real hope.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>*These DNA differences go by lots of different names: variant, SNP, mutation, mistake, etc.\u003c/em>\u003c/p>\n\n","blocks":[],"excerpt":null,"status":"publish","parent":0,"modified":1340306642,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":22,"wordCount":976},"headData":{"title":"Tackling the Cause of Cystic Fibrosis One Mutation at a Time | KQED","description":"There was big news in the cystic fibrosis (CF) field recently: a new CF drug called ivacaftor (or VX-770 or Kalydeco) has been approved that does more than target the symptoms of CF. It actually works to get the broken gene working again. The good news is that this is the first treatment that has","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"39182 http://science.kqed.org/quest/?p=39182","disqusUrl":"https://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/","disqusTitle":"Tackling the Cause of Cystic Fibrosis One Mutation at a Time","path":"/quest/39182/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_39185\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/ivacaftor/\" rel=\"attachment wp-att-39185\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/06/Ivacaftor.jpg\" alt=\"\" title=\"Ivacaftor\" width=\"640\" height=\"365\" class=\"size-full wp-image-39185\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/06/Ivacaftor.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/06/Ivacaftor-400x228.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This little molecule is changing how some cystic fibrosis patients are treated. And how new drugs may be made in the future.\u003c/figcaption>\u003c/figure>\n\u003cp>There was big news in the cystic fibrosis (CF) field recently: a new CF drug called ivacaftor (or VX-770 or Kalydeco) has been approved that does more than target the symptoms of CF. It actually works to get the broken gene working again. \u003c/p>\n\u003cp>The good news is that this is the first treatment that has the potential to cure this genetic disease (as long as the patients keep taking their medicine). The bad news is that it is only approved for around 4-5% of people with CF. This last bit of news may get a lot better in the near future but ivacaftor will never help every CF sufferer.\u003c/p>\n\u003cp>The reason for this has to do with the fact that there is more than one way to break the main gene involved in CF -- the CFTR gene -- and that there is more than one class of CFTR break.\u003c/p>\n\u003cp>The CFTR gene has the instructions for making the CFTR protein. This protein needs to get made and sent to the membrane so it can do its job of shuttling chloride ions back and forth. If you have a slight difference* in the gene that disrupts any step, then you can end up with CF. (Although not every slight difference leads to CF -- not by a long shot!)\u003c/p>\n\u003cfigure id=\"attachment_39190\" class=\"wp-caption alignright\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/cftr/\" rel=\"attachment wp-att-39190\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/06/CFTR.jpg\" alt=\"\" title=\"CFTR\" width=\"250\" height=\"230\" class=\"size-full wp-image-39190\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">There are many ways to keep this protein from working. Each way may need a different medicine.\u003c/figcaption>\u003c/figure>\n\u003cp>So some CF-causing differences in the CFTR gene will keep the protein from being made while others will keep it from making it to the membrane. Still others will keep the channel from opening wide enough to let the chloride ions pass through. Ivacaftor helps people in this last category.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>These folks have a mutation in their gene called G551D. As you might recall, genes are written in a simple language that just has four letters—A, G, C, and T. These letters are all grouped together in a gene to form three letter words. \u003c/p>\n\u003cp>With the exception of three words that act like a period at the end of a sentence, each of these words corresponds to one of twenty different amino acids. So a gene is really just the instructions for stringing together certain amino acids in a certain order.\u003c/p>\n\u003cp>The CFTR protein is made up of 1470 of these three letter words. The people helped by ivacaftor have a letter change that causes the cell to read the 551st word as a D instead of a G. This is enough to cause the protein to have trouble letting the chloride ions through.\u003c/p>\n\u003cp>Ivacaftor enhances CFTR’s ability to open up. So it makes sense that it would help people with the G551D variation. But it also makes sense why it won’t help for other CF patients.\u003c/p>\n\u003cp>For example, around 10% of people with CF have what is called a nonsense mutation in their CFTR gene. What happens in these cases is that a word that normally corresponds to an amino acid is mutated so that it now codes for a period. The cell stops reading the gene too soon and so you end up with only a part of the protein. Usually these “truncated” proteins can’t do much of anything. \u003c/p>\n\u003cp>Giving one of these patients a drug that helps the full length protein open wider isn’t going to be of much help. No, you need a drug that will ignore the period and make at least some functional CFTR. And there is a drug in the pipeline called PTC-124 that just might be able to pull this off. Of course PTC-124 will be of little use for people with the G551D variant!\u003c/p>\n\u003cp>Now having said this, ivacaftor may be more than a one trick pony. In fact, it may be able to help the majority of people with CF in the near future. \u003c/p>\n\u003cfigure id=\"attachment_39195\" class=\"wp-caption alignright\" style=\"max-width: 150px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/06/11/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time/atcgpeople/\" rel=\"attachment wp-att-39195\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/06/atcgPeople.jpg\" alt=\"\" title=\"atcgPeople\" width=\"150\" height=\"184\" class=\"size-full wp-image-39195\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Our genetic uniqueness will make finding cures more difficult.\u003c/figcaption>\u003c/figure>\n\u003cp>Most people with CF have a certain mutation called delta508. Basically the 508th word has gone missing in their CFTR gene.\u003c/p>\n\u003cp>What happens in these cases is that most of the CFTR protein gets lost on its way to the membrane. But a tiny bit does make it to the right place and ivacaftor might be able to boost that little bit enough to help these patients. \u003c/p>\n\u003cp>Ivacaftor is currently in Phase 2 clinical trials to see if it can help patients with the delta508 variant. The results are promising so far.\u003c/p>\n\u003cp>These treatments for CF are showing how we may have to deal with genetic diseases in the future. As I talked about in my last \u003ca href=\"http://ww2.kqed.org/quest/2012/05/28/why-your-newfound-uniqueness-a-nightmare-for-your-doctor/\">blog\u003c/a>, we are all unique genetically. This means that even simple genetic diseases are going to be like CF and come in many different classes that will all have to be treated differently. It also means that new drugs may only help a relatively small number of patients.\u003c/p>\n\u003cp>This last point will require a paradigm shift in how drugs are developed too. Most big pharma companies won’t touch drugs that treat so few people. Ivacaftor is showing us the way here too.\u003c/p>\n\u003cp>The Cystic Fibrosis Foundation provided big pharma with a sizeable chunk of change to get this drug through clinical trials and to the market. The new paradigm may be that interested patient groups collaborate with big pharma to get these “boutique” drugs to market. \u003c/p>\n\u003cp>It’ll be interesting to see if this is a viable business model. But at least for now a minority of CF patients can have real hope.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>*These DNA differences go by lots of different names: variant, SNP, mutation, mistake, etc.\u003c/em>\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/39182/tackling-the-cause-of-cystic-fibrosis-one-mutation-at-a-time","authors":["6177"],"categories":["quest_4","quest_12"],"tags":["quest_11181","quest_11182","quest_753","quest_11183","quest_1197","quest_11180","quest_13202","quest_3319"],"featImg":"quest_39185","label":"quest"}},"programsReducer":{"possible":{"id":"possible","title":"Possible","info":"Possible is hosted by entrepreneur Reid Hoffman and writer Aria Finger. Together in Possible, Hoffman and Finger lead enlightening discussions about building a brighter collective future. The show features interviews with visionary guests like Trevor Noah, Sam Altman and Janette Sadik-Khan. Possible paints an optimistic portrait of the world we can create through science, policy, business, art and our shared humanity. It asks: What if everything goes right for once? How can we get there? 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