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Making Sense of SNPs

This page is to explain SNPs in terms of genetic genealogy.

How are SNPs used in genetic genealogy?

A conflict in SNPs can be used to exclude the possibility of a shared direct paternal ancestor with another person. In other words, they can rule out false leads. A similarity of SNPs, though, does not by itself establish a relationship within genealogic time or have the same meaning as a STR match.

Example: My R1b Y-chromosome seemed to trace back to a particular man living in the 1600s. But a well-documented descendant of his had DNA results showing he was J2. These two haplogroups have been split off from each other for more than 20,000 years. The J2 man and I (R1b) could not have the same direct paternal ancestor who lived at late as 1600.

The above example is a difference of two major haplogroups but the principle holds even for fine-division subclades of the haplogroups.

Too many matches?

SNPs can help men with common haplotypes (say, WAMH) eliminate some of their possibly hundreds of "close matches". Suppose the guy has tested to be U106+; he can eliminate anyone who's P312+ or positive for any SNP downstream of P312. These two branches frm M269 date back at least 2,000 years.

What is a SNP?

SNP is short for "single nucleotide polymorphism". That mouthful is easier understood by breaking it down:

A SNP is a DNA sequence variation where a single nucleotide changes at a particular position . For example, at ChrY:21151206 from
      AAGCCTA to
      AAGCTTA,
The C has changed to T, so we have a SNP.

Certain SNPs on the Y chromosome have been identified as defining haplogroups and subclades. They have been catalogued and placed on the Y-chromosome phylogenetic tree.

Research is continuing.

SNP Naming

Perhaps, the most confusing part of the whole subject is how SNPs get their names. They consist of one to three letters followed by numbers.

So, "M343" (in which a C changes to T at position 2887824) was the 343rd SNP found by the research group whose code name is "M".

Multiple Names

An SNP may be found by more than one group, given a name & number by each, then discovered to be the same thing. M343 is also known as PF6242; this may be shown as "M343/PF6242".

Also, an SNP registered by NCBI is given an "rs" number; M343 is also rs9786184. (Click the link to read all about it.)

Developments

A recent move is to designate haplogroups and subclades, not by their phylogenetic names, but by the SNPs defining them. Thus R1b1a2 is now R-M269.