Pregnant Women Face Big Questions With Cheaper DNA Sequencing

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.

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.

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.

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.

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.

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.

Back in 2008, 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.

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.

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.

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.

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 this report were able to read all of a fetus’ genes base by base. They can now get a complete genetic readout of the fetus.

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…

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.

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 90% or so 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.

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.

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?