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Archiver > GENEALOGY-DNA > 2006-11 > 1163347171


From: Adrian Williams <>
Subject: Re: [DNA] Conference [recLOH]
Date: Sun, 12 Nov 2006 09:59:31 -0600
References: <539.c7d7c43.32821267@aol.com>
In-Reply-To: <539.c7d7c43.32821267@aol.com>


Y'all,

I have been able to talk with Bennett a few times this week and he
helped clear the air (and my head). Hopefully this will clarify the
information and measuring genetic distance on the palindromic markers.

Yes, measuring the recLOH is with each palindromic arm. For example,
DYS385 is on P4 while DYS459, DYS464 and CDY (DYS724) are on P1 and
YCAii is on P5. From the information from the conference that ALL
lettered markers are affected (i.e. suffixed with a letter a, b, c, etc).

And you are also correct that the recLOH is very specific...in other
words, according to Bennett, the numbers will be identical in a recLOH
event. For example, on 385 a person with 11 11 and another with 11 14.
A recLOH has most likely occurred here with the 11 14 being the
ancestral value and the 11 11 being the newly recombined value, the
genetic distance being 1. And, when I asked about a non-identical move,
for example two CDY values: 37 38 and 37 39, these do not constitute an
recLOH event and is simply a mutation.

Additionally, both Bennett and Thomas indicate that all mismatches on
a given palindromic arm that are caused by a recLOH are counted as one.

So, this is my understanding of the way we count the mismatches on
palindromic markers:

Given these results (from Thomas' presentation at the conference) of
markers that all occur on the same palindromic arm:

DYS459 DYS724 (CDY) DYS464 Genetic Distance
9-10 37-38 14-14-16-18 MODAL
9-10 37-38 14-15-16-18 1
9-10 37-38 14-14-16-18 0
9-10 37-39 14-14-16-18 1
9-10 37-38 14-14-16-18 0
10-10 38-38 14-14-18-18 1
9-10 37-38 14-16-18-18 1

In this example, Thomas has clearly indicated that a multi-marker recLOH on that same palindromic arm constitutes a 1-step mutation. So, instead of the last results set being 3 steps from the modal, it is only 1, the mindset being that the repair event occurred along all portions of that particular palindromic arm.

And you can very well have an event on one arm and not the others, which makes our mismatch determinations even more fun!
Now, using the same set and adding the other palindromic markers, you can see, each arm is counted independently.

DYS459 DYS724 (CDY) DYS464 DYS385 DYSYCA Genetic Distance
9-10 37-38 14-14-16-18 11-14 19-23 MODAL
9-10 37-38 14-15-16-18 11-14 19-19 2
9-10 37-38 14-14-16-18 11-11 19-19 2
9-10 37-39 14-14-16-18 11-14 19-23 1
9-10 37-38 14-14-16-18 11-11 19-23 1
10-10 38-38 14-14-18-18 11-11 19-19 3
9-10 37-38 14-16-18-18 11-11 19-19 3

I hope this clears my earlier confusion. There is some additional information about DYS464 and how it can exist on two different arms, but that is another discussion for another day. If someone can help clarify and/or correct this, I know I for one will be grateful as I was still in the "oh crap!" mindset when some of this was being explained during Thomas' presentation.

Kind regards,
Adrian

Adrian Williams
Williams DNA Project Administrator
http://williams.genealogy.fm/
http://www.dna-pat.com/




wrote:
> In a message dated 11/7/2006 7:53:42 AM Pacific Standard Time,
> writes:
>
>
>> It used to be that each marker set was examined separately when
>> determining mismatched markers. For example, if two kits had a marker
>> mismatch at 385, 464 and CDY, then this would be 3 steps....well, now
>> because of the discovery of recLOH, this is only 1 step...it doesn't
>> matter how many of the palindromic markers are mismatched. Any number of
>> mismatches on them results in a total of 1 step.
>>
>
> That's much broader than the way recLOH has been described previously on this
> list, and I find it puzzling. In the first place, DYS385 is on a different
> palindrome (#4) than DYS464 and CDY (#1). In the second place, only certain
> changes qualified to be examples of recLOH, e.g.
>
> DYS385a/b = 11-14 as the ancestral haplotype (two different alleles,
> "heterozygous")
> DYS385a/b = 14-14 or 11-11 as the haplotype in one branch (identical alleles,
> "homozygous")
>
> I can readily accept the above example as recLOH. It sounds like now you're
> saying that the whole set below would count as 1 step, but maybe I
> misunderstand.
>
> DYS385a/b 11-14 and 11-15
> DYS464a/b/c/d 15-15-17-17 and 15-16-17-17
> CDYa/b 37-38 and 37-39
>
> Could you give us some concrete examples of counting genetic distance? And
> what about DYS459a/b (palindrome #1) and YCAII a/b (which is on palindrome #5)?
>
> Ann Turner
>
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