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Archiver > GENEALOGY-DNA > 2007-12 > 1199088762


From: Thomas Krahn <>
Subject: Re: [DNA] Question for Thomas Krahn - STRs in WOY regions
Date: Mon, 31 Dec 2007 02:12:42 -0600
References: <11985d4c0712291203s44d3bd95l7abbffd6e7dafa01@mail.gmail.com><IGEOKAGLHNEKPCKPADIGEENIABAB.bbailey.lowedna@baileyconnection.com> <11985d4c0712291324ubd15c05sef7d91bc8b7994e@mail.gmail.com><00e501c84a62$8d998c80$6400a8c0@Ken1> <4778087C.1090103@comcast.net><008501c84b2c$d0896a90$6400a8c0@Ken1> <47784C4E.2040008@comcast.net><000001c84b75$3d06ece0$0100a8c0@john>
In-Reply-To: <000001c84b75$3d06ece0$0100a8c0@john>


Alister John Marsh wrote:
> Thomas,
>
> I don't think I have asked this on the list before, but with the "Walk On
> Y", will results be reported for any of the obscure STRs which are be in
> that section of Y?
>
Yes, as long as they give readable sequencing traces. STRs with short
repeat units (Mono- di- and tri-nucleotide repeats) and / or a high
frame shift mutation rate will show a significant amount of stutter
which mans that the sequence will be unreadable right after the last
repeat unit. Sequencing quality may go down so that one can't even count
the repeats in those cases. But in some other cases we have had
perfectly clean reads through the whole STR. It also depends on the
individual (possibly the age of the person).
> Apart from the 120 or so commonly commercially tested STRs, there are
> apparently many more STRs scattered on Y. Many of these others have shorter
> numbers of repeats, say 5 to 9 repeats. I presume these are mostly not
> commercially tested, as they are thought to infrequently mutate. However, a
> STR with say 5 to 9 repeats, may have mutated at least once in human
> history. Some estimate in the order of 6,000,000,000 male births since Adam,
> and if only 1% of those left male descendants, it is still a fair number of
> opportunities for a short STR to have mutated at least once.
>
Such short repeats exist and they are usually easy to sequence.
> My guess is that in 50,000 base pairs, there might be several short STRs,
> perhaps a few dozen if you include very short STRs and those with repeats of
> 2 or 3 bases.
>
> I have previously expressed my interest in a test company offering to test a
> panel of perhaps 50 or 100 ultra slow STRs. Perhaps WOY might produce some
> of these as a byproduct of the SNP search.
>
> It would be interesting if any STRs other than those commonly tested, were
> reported in WOY results basically as a panel of ultra slow mutating STRs,
> say STRs 68 to 77 or whatever. Whilst there would be few mutations, any
> mutations found on those would be hugely important in indicating structure
> to the Y Tree, even if they were not formally recognized as SNPs, and not
> "officially" haplogroup clade defining.
>
I agree with you and we definitely will get some STR data. However STRs
will probably not be accepted by the anthropological/scientific
community as markers of the Y tree (for whatever reason).
> In FTDNA's test runs on the WOY, I presume you would have covered ground
> including some "lesser" STRs. Are you able to indicate if there might be
> sufficient of these ultra slow STRs to form a significant panel, perhaps of
> 10 STRs?
>
>
Yes, in the trial runs we came across several STRs. One specific poly A
sequence seemed to be very variable but we couldn't count the repeats
because the sequence dropped off right at the end of the repeat (in both
directions). Several others were well readable and a few showed
differences to the HUGO reference sequence. I didn't count STR mutations
when I estimated the de-novo SNP frequency as 1-2 per 50kb from our
trial runs. However, we have had just 2 persons in the trial runs so
far, so these numbers are only "guestimates".

Thomas

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