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Archiver > GENEALOGY-DNA > 2010-03 > 1268391291


From: Wayne Kauffman <>
Subject: Re: [DNA] Genome work ushers in new genetic era- how can we minenew data?
Date: Fri, 12 Mar 2010 02:54:51 -0800 (PST)
References: <820524.38859.qm@web31507.mail.mud.yahoo.com><3480483d1003111516m21fc9650j471e81b2393618ac@mail.gmail.com><6086D865ECC142D08C3655B4A6581FD5@john><792174.52375.qm@web81705.mail.mud.yahoo.com><REME20100311213121@alum.mit.edu>
In-Reply-To: <REME20100311213121@alum.mit.edu>


John,

I have already identified 5 relevant SNPs in 23andMe results. Confirmation work is moving forward on a number of these. I am running a discovery rate of 7-9% for the submissions to my project. Let's see if I get these labeled correctly....
M228+ under S116
P36+ under J2a1b*
rs35690250+ under R1b-U106*
L86+ under S116
and what appears to be M359+ under J2a

There is a lot more to understand around how many SNPs are relevant and their prevalence even though the 23andMe sample is limited to 1921 SNPs.

- Wayne






________________________________
From: John Chandler <>
To:
Sent: Thu, March 11, 2010 9:32:25 PM
Subject: Re: [DNA] Genome work ushers in new genetic era- how can we mine new data?

Wayne wrote:
> Come up with a way for 23andMe to release all of their y chromosome
> data in order for it to be scanned for new SNPs.

23andMe doesn't do sequencing, just probing of a specific list of
already known and already studied SNPs. For the Y chromosome, I count
just 1921 SNPs reported. If we assume that they have tested 15,000
customers with Y chromosomes, the total output is only about equal to
the total number of sequenced bases in one Y chromosome. That means
there should be only a handful of novel, parallel mutations in the
whole lot. I don't know what the error rate is for their testing,
but I fear there might well be a similar handful of errors among so
many tests.

John Chandler

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