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From: (Bonnie Schrack)
Subject: Re: [DNA] DNA] Upstream I1b* clade strange doubling
Date: Tue, 14 Aug 2007 17:38:26 +0000


Ken wrote:

> I have the upstream I1b* clade (not I1a, not I1b1 (old I1b), not I1b2 (old I1c and I1-x)) already dividing into three sub-populations.
>
> One sub-population has a strange doubling. Of the 9 different surnames in it with 37 or more markers, all have double CDYa,b values, 35-35 or 36-36 or 37-37.
> These 9 haplotypes, except for one, all have double 459a,b values, 9-9 or 10-10 with a single 9-10
> But 464a,b,c,d does not look unduly doubled up. So perhaps a special kind of extensive deletion which hit just CDY and 459 may have occured.
>
> A question for those who have mastered the geography of the pertinent palindrome: are there other advanced multi-copy markers worth measuring which stand a good chance to show doubling as well?


Maybe I shouldn't, but I'll take a shot at it. This may just show my relative lack of knowledge, but it looks to me as though DYS724 (CDY) and DYS459 are very near eachother on the P1 palindrome, when it's folded with its two arms together in the normal position (rather than the alternative one). In between those two markers, the only marker shown is DYF385. So if there were a recLOH or something affecting that little region, it should affect DYF385 as well. Trouble with that is, I don't know what you have in I, but in J, all our test results show 10-10 at DYF385 anyway, (or 10-10-10 in the case of extra copies), so you couldn't tell in that case whether anything special had happened.

DYS464 is located at a bit of a distance on another part of P1, so it would make sense to me that it wouldn't be affected.

Flanking DYS724 on the other side is DYF371 (two of the c-type alleles, not all four alleles). So you could check that as well to see if it's affected, though it might be hard to tell, since I can see quite a few haplotypes in which there are two identical c alleles there without there being any doubling at DYS724 or 459. On the other side of DYS459 is DYF387, which is not currently offered for testing. The next one if we continue in that direction is DYF401. That marker does show interesting variation, so I would check that one if I were you.

Hope that is helpful. I imagine Gareth, and of course Thomas Krahn, could shed much more light on this.

Bonnie


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