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Let's imagine a family composed of Mr A and Mrs B, who have a son named John.

Now, if for whatever twisted reason, John had a child with Mrs B, could a paternity test yield positive result for Mr A ?

Since John's genes all come from Mr A and Mrs B, the child's genes would all come originally from Mr A and Mrs B as well. Thus it seems to me like the test could suggest Mr A is the father of the child.

Or would there definetly be some "red flags" that suggest something wrong happened ? Like, for example, if the child is a girl, that would mean both of her X chromosomes originally came from Mrs A (since John's X chromosome comes from his mother, as for all males), possibly even the same chromosome twice.

Let's consider that only Mr. A is tested, and not John. Would the child be considered genetically close enough to Mr. A that a test could attest that he is probably the child's father, granting there is no other test showing someone else as a much more likely candidate ?

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Let's approach some different methods of distinguishing parents:

1: The Y chromosome. These are passed down from father to son. Therefore, if the baby is male, its Y chromosome will be the same as John's and his father's - it will be indistinguishable who it's from.

2: The X chromosome. A male baby always has one of the mother's X chromosomes. A female baby always has its father's X and one of the mother's X. A male baby of John and Mrs B would always end up with one of Mrs B's X chromosomes, meaning that this can't distinguish the father. A female baby would have two X chromosomes from Mrs B (because John's own X came from her), proving that it is the product of incest.

3: Mitochondrial DNA. mtDNA is passed on from mothers to their children, never from the father. Therefore regardless of whether John or Mr A is the father, the baby would have Mrs B's mtDNA - not useful.

4: DNA fingerprint. This is primarily based on stretches of the human genome that contain repeats of short DNA sequences (so-called STR/short tandem repeats, or VNTR/variable number tandem repeats). In both cases, the sequence is the same in individuals, but the number of repeats is extremely variable and each human therefore has a (possibly) unique combination across the different repeat locations in the genome. Because children inherit 50% of their DNA sequences from the father and 50% from the mother, John himself will have his mother's characteristic lengths in 50% of repeat locations and his father's in the remaining 50% of locations (roughly). A child of John and Mrs B would have MrA's repeat lengths in 25% of locations and Mrs B's in 75%. The fractions "100% Mr A" vs. "50% Mr A" vs. "25% Mr A" can be distinguished by this method.

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No, Mr. A would not be flagged the father. This is becasue when a parental test is done they look to what genes have the mother, the father and the baby. First they look at what genes has the mother and the baby. The one missing should be from the father.

In this case it could be possible that for example:

Mr. A: 1 gene Red hair, gene Blond hair.
Mrs. B: gene Brown hair, gene Black hair.
John: gene Brown hair (from his mother), gene Blond hair (from his father).

If the baby has: gene Black hair (from mother) and gene Brown hair (from John. Then that would prove the hair color is not from mr. A. He doesn't have those genes. So he isn't the father.

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    $\begingroup$ This answer is technically inaccurate. DNA testing doesn't work like this. $\endgroup$ – anongoodnurse Jan 18 '17 at 14:43
  • $\begingroup$ @anongoodnurse, you say it doesn't work like this, downvotes my post, and then you forget to post how it is done yet... Why don't post how it is done then? It is very easy to say 'You are wrong', but then come with arguments to support your argument. :-) $\endgroup$ – Tenzin Jan 18 '17 at 15:14
  • $\begingroup$ The way it is done has already been explained in the other answer. No need to repeat. The gist is the child-mother offspring will have approximately 75% maternal DNA and 25% (original) paternal DNA. $\endgroup$ – anongoodnurse Jan 18 '17 at 15:17
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    $\begingroup$ @Tenzin, there are an infinite number of wrong answers. It is not our responsibility to prove them all wrong, it is your responsibility to justify your answer and provide citations. $\endgroup$ – Scott Jan 20 '17 at 9:27

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