Minding the base rate fallacy

In the near future, I’m pretty sure that most pregnancies will begin with a non-invasive genomic analysis (OK, that’s not how they will really begin, but you get what I’m saying). Far more extensive than what you get now no doubt.

But, non-invasive prenatal tests (NIPT) is already ubiquitous for a variety of conditions, in particular, those that result in visible changes in the karyotype. Down syndrome is probably the most well-known instance of this, though there are others. Denmark funds NIPT through public monies, and Down syndrome has almost disappeared among children born.

With all that being said, the presentation of results from these tests must be accompanied by some statistical scaffold or primer. Here is a post from someone with a background in computational genetics, How I learned to stop worrying and love Bayes’ Theorem:

At my 9 week doctor’s appointment, my doctor brought up the option of genetic testing, specifically non-invasive prenatal DNA testing. As a geneticist doing bioinformatics, I thought how cool it is that we can test for chromosomal abnormalities from the blood of the mother. The idea is that there are fetal DNA floating around in the mother’s blood and so inferences about whether there is an excess of a particular chromosome can be made by examining the mother’s blood…

Fast forward 2 weeks, I was at a FedEx store faxing my medical record to the doctor’s office at UCLA (I was in Boston for an internship for a few weeks during my first trimester) when I got a phone call from my doctor in Boston. This was the most difficult phone conversation I have ever had in my life. Over the phone, she told me that the NIPT test came back that my baby was high risk (40% chance) for Trisomy 13 (or Patau’s syndrome). My heart dropped….

Some of you see the title of this post. And you see the title of the post I linked to. So you know the conclusion and the moral of the story.

If you are still confused, please do read the post, and afterward please do repeat the phrase “base rate fallacy” to yourself multiple times, because it will prevent you from getting confused. It’s in the class of “news we’ll need to use” in the near future.