Are there any good prenatal paternity tests out there?

December 19, 2012

Related Topic:
Paternity tests

A curious adult from California asks:

"Are there any good prenatal paternity tests out there? I want something safe, reliable and easy to understand."

Until recently, figuring out who the father of a child was before the child was born was not easy.  The most reliable method meant getting DNA from the fetus using an amniocentesis or chorionic villus sampling (CVS).  These are very reliable but there is a real risk for miscarriage.

Other problems with these methods include the fact that they can only be done when a woman is pretty far along in her pregnancy. Additionally,  they are invasive and not cheap.  Women and their potential partners needed better prenatal paternity tests.

These better tests became possible when scientists discovered that there were small amounts of the baby’s DNA floating around in mom’s blood. Various groups have since tried to use this DNA for a paternity test with varying amounts of success. 

I talked about one of the most high powered methods recently and so won’t go into it in any more detail here.  This method was originally used to test for various genetic problems in the fetus but has now been adapted for prenatal paternity testing too. 

A new test that recently came on the market is much easier to understand.  It basically looks for DNA unique to dad in mom’s blood.  Since this DNA isn’t found in mom, it had to come from the fetus.

The DNA from the fetus is then compared to a potential dad’s DNA.  If a lot of the fetal DNA matches up with a potential dad, then there is a good chance that the man is the dad.  If there aren’t enough matches, then he probably isn’t the biological father.  

This is pretty easy to understand but not so easy to pull off.  What I’ll do for the rest of the answer is go into a little more detail about the test and what it took to get it to work well.  As you’ll see, they needed to deal with two major problems:

  1. The fetal DNA in mom’s blood is present in very tiny pieces
  2. There is an overwhelming amount of mom’s DNA in her blood

Dad + Mom = You

You may have heard that you get half your DNA from your mom and half from your dad.  What you might not realize is that each parent gives you a complete set of DNA. 

What this means is you have two copies of most every one of your genes too.  Let’s see what this means for a paternity test.

A paternity test subtracts mom’s DNA from the child’s and compares what is left to dad’s.  The more of dad’s DNA that matches the child’s, the more likely he is to be the dad.

Well that was probably clear as mud.  I think an example might help.  For this I’ll focus on a single spot on the DNA.  Imagine the following results for mom, child and two potential dads:

DNA Marker



Potential Father 1

Potential Father 2


9, 13

13, 14

13, 14

9, 13

 We are looking at a single spot on the DNA, D8S1179 (clever name, huh?).  A small bit of DNA is repeated over and over at this spot and different people can have different numbers of repeats.  The number in the table refers to how many repeats there are.

So one copy of mom’s DNA has 9 repeats and her other copy has 13.  Remember, mom passes down just one of her copies to her child.  To figure out which one, we need to next look at the child’s DNA.

The child has 13 repeats on one DNA and 14 on the other.  Mom and the child share the 13 so that came from mom.  So now we know that the potential dad has to have a 14 to be the dad.  In other words, the child’s 13 came from mom so the 14 had to come from dad.

When we look at the two potential dads, we see that only potential dad 1 has a 14 to give.  This means he is more likely to be the dad than potential dad 2.  Note the more likely

A paternity test needs to look at more than a single spot because lots of men will have a 14.  In addition, for reasons I’ve talked about here, a single mismatch like this is possible even with the real dad.  This is why a good paternity testing company looks at lots of markers and gets some information about the potential dads whenever possible. (Click here for why this is important for the second part.)

Making it Work Prenatally

The kind of paternity test I described in the last section works really well after the baby is born.  But it is pretty useless for the fetal DNA found in mom’s blood.

First off, this fetal DNA is in lots of tiny pieces.  In fact, the DNA bits are so small that they are not big enough to see the repeats usually used in a paternity test.  This means you can’t get an accurate read looking at repeats.

That is why this prenatal paternity test focuses on much smaller differences.  Instead of looking at differences in numbers of repeats, it looks for differences at a single letter of DNA.

You may recall that DNA is made up of four different subunits that are referred to as A, G, C, and T.  So what the test looks for are differences at a single one of these letters.  Maybe mom has an A at a certain spot and dad has a G.

So this solves the fetal DNA being small.  The next big hurdle is that there is a whole lot more of mom’s DNA in mom’s blood than there is the baby’s DNA.  This means that mom’s DNA tends to overwhelm and swamp out the baby’s DNA.

To get around this problem, the test focuses only on those differences where mom’s DNA is completely different from dad’s.  That way, if they find a hint of DNA different from mom’s DNA in mom’s blood, then it most likely came from the fetus.

What this means in practice is that the test only looks at spots on the DNA where mom has two copies of one letter and dad has two copies of a different letter.  In genetics, this is called being homozygous at this allele.

Here is what the result might look like:

DNA Marker


(Mom’s Blood)

Potential Father 1

Potential Father 2

Marker 1

A, A

A, G

G, G

A, A

Notice that mom has an A on each of her copies of this marker.  The potential dad’s have either two G’s or two A’s. 

Mom’s blood is mostly A but there is a wisp of G in there too.  Since mom is AA, this G most likely came from the fetus.

We next look at the two potential dads and see if either has a G to offer.  We see that potential dad 1 has a G but potential dad 2 does not.  Because of this, potential dad 1 is more likely to be the dad based on this position.

As I said before, one marker is not all that useful in establishing paternity.  Which is why the test looks at many other markers until they are at least 99.9% sure that one of the men is the dad.

So far the results with this test have been encouraging.  If they continue to hold up, pregnant women and their potential partners may finally have an easy to understand, safe, and reliable prenatal paternity test.

Author: Dr. Barry Starr

Barry served as The Tech Geneticist from 2002-2018. He founded Ask-a-Geneticist, answered thousands of questions submitted by people from all around the world, and oversaw and edited all articles published during his tenure. AAG is part of the Stanford at The Tech program, which brings Stanford scientists to The Tech to answer questions for this site, as well as to run science activities with visitors at The Tech Interactive in downtown San Jose.

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