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From:
Subject: Re: [DNA] Comparison of deCODEme results for the Y-chromosomeofR1b1c7and R1b...
Date: Mon, 25 Feb 2008 12:59:27 EST


In a message dated 2/25/2008 8:28:02 AM Pacific Standard Time,
writes:

> I'm not sure about the discrepancy in the number of SNPs tested and the
> number of SNPs reported for the two men I know about. I think there are some
> duplicates involved in the locus list, but I don't know how many. Ann Turner
> did a study of Illumina SNPs in the ISOGG tree and removed duplicates. I
> don't know what the statistics of this were. She may have meant that
> parallel SNPs for a given clade label were not reported if they were
> duplicates.

By duplicates, I was referring to the RefSNP ID column in the ISOGG tree,
where the same SNP might show up more than once, e.g. attached to markers in the
M and P series. I just gave one AKA marker name in the spreadsheet I uploaded.

http://members.aol.com/dnacousins/ISOGG_SNPs_in_deCODEme.xls

I don't know why deCODEme is not reporting all the results from the Illumina
BeadChip, but I can speculate <g>. It's possible that the missing ones simply
turned out to be too problematic for that type of assay. Even with the current
set of reported SNPs at 23andMe, which could already be weeded down from all
the ones they requested, there were a certain number of no-calls, which differ
from person to person.

There are several of you who are interested in mining the deCODEme results. I
have a couple of more thoughts on this. Perhaps all of you could declare
yourselves to be a committee.

As I mentioned before, right now deCODEme is not reporting very deep levels
(e.g. just R1a and R1b). Someone forwarded me an e-mail from a deCODEme tech
support person, which hinted that they are working on a more complete tree
themselves. They might welcome collaboration with the genetic genealogy (or not) --
but I could certainly forward an expression of interest from a committee.

The Illumina SNPs were probably gathered willy-nilly from various sources,
undoubtedly including the Perlegen discoveries, which were uploaded to dbSNP
several years ago.

Does anyone know whether the new YCC phylogenetic tree to be published by
Hammer will include more citations to dbSNP? There has been a relative paucity of
P series markers with rs numbers to date. I wonder if it would pay to hold
off until that paper is published and/or deCODEme updates its tree structure.

I have uploaded a spreadsheet with 23andMe SNPs for my husband Jim, Brian
Smolenyak, and 23andMe's demo user, an I1. It's a work-in-progress, as I just
picked a few random SNPs from the Underhill paper for the haplogroup column.
Maybe I could prevail upon "the committee" to complete it for me :)

http://members.aol.com/dnacousins/23andMe_Y_SNPs.xls

Ann Turner




Ann Turner





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