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Archiver > GENEALOGY-DNA > 2008-01 > 1199315385


From: Gareth Henson <>
Subject: Re: [DNA] Chances for Finding Clade-separating SNP
Date: Wed, 02 Jan 2008 23:09:45 +0000


Tim

the non-R1b1c region spans at least positions 12943108 to 13540810 because rs2740981 at 12943108 is ancestral G in HUGO but derived A in all the R1 samples in the Hinds and Underhill/Kivisild papers. However M207 at 14091377 is derived G in HUGO so the region probably doesn't extend to that point.

The following paper suggests AFZa spans about 800kb:
http://hmg.oxfordjournals.org/cgi/content/full/9/15/2291

Gareth


On Wed, 2 Jan 2008 11:06:03 -0800 , "Tim Janzen" <> wrote:
>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
>To:
>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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