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Archiver > GENEALOGY-DNA > 2006-04 > 1146371059


From: "Joe Fox" <>
Subject: Re: [DNA] Re: R1b SNP page updated
Date: Sat, 29 Apr 2006 21:29:05 -0700
References: <E1FZx2O-000KvG-QP@mk-webmail-1.b2b.uk.tiscali.com>


Thanks, Gareth

I can see now that I misunderstood what John was saying about S21.

Joe Fox
Lafayette, CA
----- Original Message -----
From: <>
To: <>
Sent: Saturday, April 29, 2006 2:31 PM
Subject: Re: [DNA] Re: R1b SNP page updated


> Ken
>
> no, S26 is a special case - it is the "DYS439 null" phenomenon, and was
> discovered precisely because it affected the testing of a nearby STR. Most
> SNPs will not be anywhere near a STR and so won't be discoverable in this
> way.
>
> My comment just meant that we know S26 is single copy because of the way
it
> was discovered, and so it can't revert by recLoH.
>
> Gareth
>
>
> ----- Original Message -----
> From: "Ken Nordtvedt" <>
> To: <>
> Sent: Saturday, April 29, 2006 10:23 PM
> Subject: Re: [DNA] Re: R1b SNP page updated
>
>
> > Did you mean to leave the impression that all known SNPs are
"associated"
> > with STRs? I guess that could be the effective situation if all
searches
> > for SNPs up until now have been done near STRs, but I did not know that
was
> > the case, although searches near STRs could be common.
> >
> > Ken
> > ----- Original Message -----
> > From: <>
> > To: <>
> > Sent: Saturday, April 29, 2006 3:16 PM
> > Subject: Re: [DNA] Re: R1b SNP page updated
> >
> >
> > > Joe
> > > gene conversion is one form of recLOH and it can happen in P25 because
P25
> > > is actually a 3 copy locus, only one copy of which has a SNP. So the
SNP
> > > is occasionally reversed when one of the unmutated copies overwrites
the
> > > mutated one. IMO if this was a newly discovered variation it would not
be
> > > acceptable as a haplogroup branch defining SNP. (Yes - we have just
> > > published a new version of the tree and P25 is still there but despite
the
> > > many changes we have had to be quite conservative in places).
> > > S21 is different, it is a single copy locus and I do not believe it
has
> > > been observed to revert. All SNPs can revert in principle but without
a
> > > backup copy elsewhere the chances of this happening are very very
small. I
> > > think John meant that P25 could revert equally in men who are S21+ and
> > > S21-, not that S21 would revert as well.
> > > I assume S26 is similarly stable as it is associated with a single
copy
> > > STR. SNPs associated with multicopy STRs will be subject to gene
> > > conversion - e.g. the G to C SNP underlying the DYS464X test sometimes
> > > appears in two copies or all four copies rather than the usual three
out
> > > of four.
> > > Gareth
>
>
> ______________________________

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