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From: <>
Subject: Re: [DNA] Re: DYS390 - Is it hiding polymorphc forms?
Date: Fri, 27 Jan 2006 20:18:58 -0000
References: <d7.356b0025.310bc823@aol.com> <000a01c62378$ca486e70$bec79045@Ken1>


Ken & List

see table 1 in the following paper for some examples of DYS390 broken down
into its constituent sections.
http://www.journals.uchicago.edu/AJHG/journal/issues/v67n1/001594/001594.htm
l
Peter Forster seems to have been the only one who followed this line of
research for a while in the late 90s (and he was part of the Jefferson
research team). There are just 3 SNPs (YAP, SRY1532 = SRY10831 and 92R7) but
with the population origin this gives some idea of the haplogroup. There is
some indication that both the "m" and "n" sections contribute to the
variability but much more from the longer "n" section.

Here is an earlier paper by Forster et al. which focussed on specific
differences in what I think we now know as haplogroup C2 amongst Aboriginal
Australians and Papuans.
http://mbe.oxfordjournals.org/cgi/reprint/15/9/1108
This seems to be a bit like the DYS455=8 in hg I1a - a rare deletion event
which produces alleles which are strongly correlated with a particular
subgroup.

I suspect that this could not be done very easily on a commercial scale.
Perhaps Thomas at DNA-FP might have some ideas on whether it could be a
specialist test. But I agree with Ann - DYS449 would be much more useful
together with CDY/DYS724 which has a similar double repeat structure.

Gareth


----- Original Message -----
From: "Ken Nordtvedt" <>
To: <>
Sent: Friday, January 27, 2006 7:35 PM
Subject: Re: [DNA] Re: DYS390 - Is it hiding polymorphc forms?


> Thank you for pointing out DYS449. It might be a more productive place to
> find sub-populations.
>
> But getting back to DYS390; it would seem an ideal place to conduct a
> relatively controlled study of the duplication machinery's error rate on
> the short segments versus the long segments? There is not a world of
> difference in the mutation rates of (fast) 449 versus (middly) 390 ---
.0065
> vs. .0044
> So looking at one versus the other does not seem on the face to be that
> different in flow of data. If the conventional wisdom that all the 390
> mutations would be occuring in the longest segment were not true, 390
would
> have a much richer set of sub-populations.
>
> I already have one lab's price for sequencing my 390. And I am waiting on
> another lab to give me a price for 390 (or 449) sequencing. My curiosity
> has been wetted.
>
> Ken
>
>
> ----- Original Message -----
> From: <>
> To: <>
> Sent: Friday, January 27, 2006 12:01 PM
> Subject: [DNA] Re: DYS390 - Is it hiding polymorphc forms?
>
>
> > Ken writes:
> >
> >> I came across SMGF's description of STR DYS390 recently on their
website.
> >> Apparently, this STR consists of a string of different actual repeats,
> >> with
> >> the quoted "repeat" being the total. Their example was a DYS390 = 25
> >> actually
> >> being perhaps 8 repeats of "TCTG", then 12 repeats of "TCTA", then 1
unit
> >> of
> >> "TCTG", and finally 4 repeats of "TCTA" for a total of 25 repeats.
> >
> > I have a very vague recollection of some early papers that did break
down
> > DYS390, but I could be experiencing some mental cross-talk with DYS389,
> > which
> > certainly been broken down into subparts, as in the Jefferson study.
> >
> > As Doug mentioned, sequencing the PCR product would be one way to check
> > the
> > internal structure. However, it might not be very cost effective. The
> > mutation
> > rate for short repeats seems to be quite low, so the bulk of the
variation
> > could be coming from the longest repeat. The sequencing approach might
be
> > more
> > productive for a marker like DYS449, one of the fast moving markers with
> > two
> > longish repeats embedded in it.
> >
> > http://smgf.org/marker_details.html#DYS449
> >
> > Ann Turner
> >
> >
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>
>
>
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