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Archiver > GENEALOGY-DNA > 2008-01 > 1199300763


From: "Tim Janzen" <>
Subject: Re: [DNA] Chances for Finding Clade-separating SNP
Date: Wed, 2 Jan 2008 11:06:03 -0800
In-Reply-To: <cd3.2678146f.34acd41e@aol.com>


Dear Ann,
It would be very helpful to know exactly which portions of the HUGO
Reference Sequence were from a different male other than the primary R1b1c
male. As I pointed out in a recent message it would appear that at least
from position 13535818 to position 13540810 of the HUGO Reference Sequence
is from a male in haplogroup G. Per the source you sited below 9 of the 11
clones were used to help span the AZFa region. I don't know that much about
that region, but I do know that it is located in the Yq11.21 section of the
Y chromosome. Per Thomas Krahn's Y browser the Yq11.21 region is in the
area between about position 12500000 and 14300000 of the Y chromosome. Note
that the section that is from a male in haplogroup G is in the Yq11.21
region. It is thus probable that one of the 9 clones that were used to help
span the AZFa region was from a male in haplogroup G. AZF stands for
Azospermia Factor. Perhaps someone on this list can tell us more precisely
the boundaries of the AZFa region.
My suspicion is that the sections of the HUGO Reference Sequence
that are from males other than the primary R1b1c male tested are relatively
small, probably not totally more than 1 million base pairs. Perhaps someone
who has connections with the Human Genome Project could inquire about this
and give us more precise information. Ideally, it would be nice to find a
male who is reasonably closely related to the primary R1b1c male in the HUGO
sequence and then compare that person's Y sequence with the HUGO sequence.
Any differences could be noted and those SNPs could be compared to other
reference sequences to see if they were from a haplogroup upstream from
R1b1c. It would be helpful to have a revised HUGO Reference Sequence that
as much as possible is from only one male that genetic genealogists could
use as a reference standard in similar fashion to how we use the revised CRS
as the reference standard for mtDNA.

Sincerely,
Tim Janzen

-----Original Message-----
From:
[mailto:] On Behalf Of
Sent: Wednesday, January 02, 2008 3:49 AM
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Subject: Re: [DNA] Chances for Finding Clade-separating SNP

But... most of it is from a single male. Quoting from Skaletsky, "All MSY
BACs selected for sequencing were isolated from the RPCI-11 library, with
the exception of 11 clones (nine spanning the AZFa region, and two used to
narrow gaps) from the CITB and CITC libraries... Unfortunately, no cell line
is available from the donor of the RPCI-11 BAC library."

http://www.nature.com/nature/journal/v423/n6942/pdf/nature01722.pdf

Maybe the Y-DNA experts on the list can pinpoint which regions contain the
exceptions?

Ann Turner



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