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Prenatal Paternity Test


julius01

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Hello, I am looling for some information regarding pre-natal DNA paternity testing. This testing hasn't been around forever and I would like to understand it a bit more. Please consider the following scenario.

 

  • The sampling method was Bucall cells from father and blood from mother.
  • "DNA was isolated from the buffy-coat samples of the mother and the buccal cells of the alleged father. DNA was sequenced at numerous single nucleotide polymorphisms (SNPs) located on multiple chromosomes throughout the human genome. The plasma DNA, which contains both fetal DNA and maternal DNA, was analyzed at the thirty two (32) informative SNPs."
  • "Among the thirty two (32) informative SNPs that were analyzed, eleven (11) fetal alleles did not match the alleged father."

So the alleles did not match the alleged father on 11 of the 32 alleles. Now I know the probability can't be as simple as dividing 11/32 here but I am unsure of how if 11 of 32 did not match they are able to conclude this alleged father is not the father with such high confidence (about 99%). What about the other 21 alleles? What is the sampling error?

What are the chances of this test being much less accurate than claimed (99%)? From what I can tell they do not accept these tests in court either as readily or at all when compared to traditional post-birth dna testing, why is this?

Thanks so much for any additional information anyone can offer.

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It depends a bit on the test method, but to put it simple, any allele found in a child has to originate either from mother or from the father. Thus if a child as alleles that are not maternal but also not from the tested father, the biological father must have been someone else. Depending on how well the lab performs and whether repetitions were done, a single mismatch may be down to some measurement error, but eleven missing alleles would be very odd. A few matching alleles are almost always expected as we are all related to some degree with each other (i.e. these are just random hits).

 

BTW, the way the procedure is described appears to be incomplete as you would need the DNA of mother, father and child. To get the latter a blood sample would not work as it would contain just the maternal DNA. Instead, generally amionotic fluid or placenta tissue has to be sampled.

It may depend on the country, but I would assume that if these tests are used for legal reasons sampling must be done under controlled conditions, especially as the sampling of the child is not as trivial as after birth (where you can simple use a swab, for example). There may be other legal reasons involved, however.

 

Once the sampling is done and assuming that it is done properly, the procedure is basically the same as for traditional tests, with the same level of inaccuracy and potential sources of error. Also, depending on what alleles are being selected certain populations may get odd results (e.g. when there is a high level of relatedness).

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Thank you for the reply. This is not a hypothetical situation as you may have guessed and this is US based. I won't get too much into the testing as far as companies go but they actually extract the fetal DNA from the maternal blood before birth, or that is what they claim to be able to do, and then try to use this baby DNA and match to the alleged father. We used two companies and the first company failed inexplicably in 3 attempts (3 new maternal blood samples) to provide anything conclusive; they ultimately said they could not do it for some reason. Company two came back the first time with the results I listed. I posted this question because I don't know how accurate a test like that could be and am a novice to genetics. I am uncertain of this method I outlined and which gave these results, as it is much less common than testing the alleged father and baby directly.

 

Once the baby is born it would be more straightforward with sampling the baby directly and matching that sample up with the alleged father of course, and this is the plan. However, in the mean time, knowing that the DNA match was done by extracting the fetal DNA signature from the mother's blood can we deduce anything about the accuracy and potential for errors?

 

I don't know if this is significant but I believe the mother is also Rh- and the father Rh+, her Dr. had advised her in the past to get shots to become pregnant so her body would not reject the pregnancy. Not sure if this is significant either but both of the alleged fathers share a similar heritage but are not related directly. For this and the reasons outlined I am unsure of the potential for error in the accuracy of this test, and welcome any comment.

 

A baby-to-father test will be conducted when the baby is born to be certain but in the meantime I wanted to get a better feel for how accurate this test may be.

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I think the test may be based on the fact that few fetal cells are found in maternal blood. While less invasive it is also quite trickier to do. However, I do not know what the potential error sources of this method are compared to more traditional sampling methods. Due to the sensitive nature of this issue I would advise you talk to the analysts directly.

It should be noted that all tests have a certain error rate (obviously). It will also depend on what guidelines the lab follows to ensure that e.g. negatives are true negatives and not e.g. just a failure in their PCR (e.g. what did their positive control look like and have they done replicates, is it a certified lab, etc.).

 

I should add that obviously an forums you will only find general info and speculations on paternity testing. What precisely went down should be cleared with the service provider and no advice or info on a web site should be taken as serious advice.

Edited by CharonY
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Thank you again for the reply. The best option is the 2nd post birth testing that will occur. Speaking with the company would only confirm the results they gave because of that natural bias to support their work and as you say, forums are purely speculation. Nevertheless, I do understand the alleles better from posting here so I thank you.

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