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Archiver > AUTOSOMAL-DNA > 2014-04 > 1396597276


From: "Tim Janzen" <>
Subject: Re: [AUTOSOMAL-DNA] The significance of segment overlaps
Date: Fri, 4 Apr 2014 00:41:16 -0700
References: <6420670.2501550.1396584058103.JavaMail.root@vznit170158><885498EC-D0D1-47A8-AC82-34F107C8B01B@ucla.edu>
In-Reply-To: <885498EC-D0D1-47A8-AC82-34F107C8B01B@ucla.edu>


Dear Don and Jim,
In general I agree with Jim's comments as well. One of the issues we
frequently struggle with as we look at HIR data is the issue of the overlap
between HIRs. My impression for HIRs that are IBD is that the portion (or
tag) of an HIR that is IBS at one or both ends is relatively short, less
than 50 SNPs or so. In an effort to gather a little more data on this, I
just ran comparisons between twenty people who share an HIR at the same
location with both my mother and me at 23andMe. These HIRs ranged in length
between 5.5 and 13.9 cMs and between 741 and 2645 SNPs. I found that the
range for the difference in the number of cMs my mother and I shared with
these matches was 0 cMs to 2 cMs. I found that the range for the difference
in the number of SNPs my mother and I shared with these matches was 0 SNPs
to 338 SNPs. The average number of cMs in these HIRs in which my mother and
I differed with these matches was .35 cMs and the median number was .2 cMs.
The average number of SNPs in these HIRs in which my mother and I differed
with these matches was 68 SNPs and the median number was 44 SNPs. Thus,
this data confirms my previous impressions. However, the one outlier where
the HIR for the match differed by 2 cMs and 338 SNPs does make one pause to
contemplate this situation. In some cases there can be a crossover on the
segment in question that causes the HIR to slightly shorter in the child
than in the parent. However, in this situation, the HIR was longer for me
than for my mother, thus ruling out the possibility of a crossover. A
genotyping error in the parent's data or in the match's data could also
explain at least some of these situations. In any case, there may be some
overlap in terms of the HIRs we see in our triangulated groups. I continue
to find that the use of children with one or both of their parents is very
helpful to me in terms of separating the parents' matches into the
appropriate triangulated group, particularly in Family Finder where you
can't run direct comparisons between your matches as you can in 23andMe.
Sincerely,
Tim Janzen

-----Original Message-----
From:
[mailto:] On Behalf Of Don Worth
Sent: Thursday, April 3, 2014 9:39 PM
To:
Subject: Re: [AUTOSOMAL-DNA] The significance of segment overlaps

Thanks, Jim. It seems like we are pretty much in agreement.

One interesting comment you made was that your TGs can contain two segments
that do not overlap at all - the first segment(s) in a TG and the last
one(s). I see this all the time in my ADSA outputs. The segments "march"
across the page from left to right and by the time the later ones start the
early ones have ended (if they are short) or, at least, they don't overlap
the early ones by much at all. This, of course, affects the ICW outcomes
since the early ones don't (necessarily) ICW the later ones. In ADSA the
rectangular block of little colored bricks kind of "flakes" away at the
upper left corner and the lower right corner so that it's not a perfect
rectangle of ICWs.

It feels a little "transitive" to presume that the early ones and the later
ones are part of the same ancestor's segment. I guess I could go either way
on that. I worry about two very different ancestral-segments lying side by
side abutting each other with little match-segments spread out across them
like overlapping shingles. If even one segment in the middle doesn't overlap
the next (or has fuzzy boundaries) this scenario seems possible.

Don



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