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From: Jim Bartlett <>
Subject: Re: [AUTOSOMAL-DNA] The significance of segment overlaps
Date: Thu, 03 Apr 2014 23:00:58 -0500 (CDT)


Don;

I'll add some of my thoughts and experience [in brackets] in your email
below

Jim Bartlett

On 04/03/14, Don Worth<> wrote:

I think this question has been asked in various ways in other forums, but
I'm trying to get a more precise understanding before I start promulgating
incorrect information to groups that I'm presenting to over the next few
weeks.
We all know about John Walden's little table that indicates the likelihood
that a segment of a given length is IBD or non-IBD (IBS). For example: a 7
cM segment is 30% likely to be IBD while a 5 cM segment is only 5% likely to
be IBD. [Tables of this type depend on the algorithm used by the company -
FTDNA uses a multipart algorithm and has fewer IBS, than say GEDmatch, for
instance. Someday I may try a table for each company - I am in the process
of culling out a lot of IBS segments - almost all below 10cM]
Can anyone opine on these questions on the basis of their experience?
1 - Does the fact that two segments overlap and the corresponding matches
are ICW affect the probability that a segment is IBD? [I definitely think
so! If several overlapping segments are all on each other's ICW list - I
think they are Triangulated over 90% of the time] For example, if you have a
Triangulated Group (TG) with two or more overlapping segments in it that all
ICW, and you find a, say, an overlapping 7 cM segment that ICWs as well - is
it more likely than 30% to be IBD? [In my opinion, folks - particularly
distant cousins - who are ICW on overlapping segments almost have to all
have IBD segments. Think about the 1,000 or so SNPs in those segments which
are all the same. When several folks have the same series of segments, they
got it from the same ancestor]. What about a 3 cM segment that is completely
overlapped and ICW with a TG? [If it matches with everyone who overlaps it,
then even a 3cM segment would be in the TG. As you get into the 3cM range,
however, the chance of an IBS segment grows - shorter segments are just
easier to fabricate and make into matches - so it's a judgment call. Some
3cM segments are IBD, so Triangulation is a good clue as to which one. There
are NO hard rules (that I know of), however, that MAKE a certain segment be
IBS or IBD]
So how small can a segment be and still participate in a TG? [see above -
use your judgment - which comes from experience - which provides plenty of
mistakes....]
2 - How much must a segment overlap another to be considered "overlapping"?
(assume the matches involved ICW) Is the area of overlap governed by John
Walden's predictions? Or do you consider the entire length of each of the
segments that partially overlap one another?
[As a general (repeat general) rule, I try to have the overlap meet my 7cM
baseline for most Matches. Someday, when I'm about 90% mapped and confident,
I'll go back and see what 5cM segments "fit". Or, on occasion, with a know
close cousin, or some tantalizing segment, I'll try some 5cM segment to see
what pops up - I really miss the GEDmatch segment utility. If you start to
develop a solid TG with 5-10 Matches with segments mostly over 10cM - in
other words you become confident in the TG - then you can deviate a little.
If they are all ICW, you can deviate a little more. Use judgment, as, again,
there are no hard rules that the DNA has to follow. As you look at all
the overlapping segments in a given area of a chromosome, each one does have
to obey one rule - they are on one chromosome or the other. I extrapolate
this like so: each segment should by in TG-A or TG-B or be IBS or be
UNDETERMINED (there is not enough info to confidently place it in one of the
other 3 groups - wait: new Matches/segments are coming every week)]
So how much of an overlap area must there be for a segment to be considered
overlapping another to form a TG? [7cM]
I had been working on the assumptions that:
A. Short segments are more likely to be IBD if they are part of a TG
(although I don't know that I would go as far as to say a 3 cM segment was
IBD - especially since the reason you ICW the owner of that segment is
probably due to a longer segment somewhere else that could be associated
with a different ancestor). [I generally agree with this]
B. The overlap must be sufficient to stand on its own as a likely IBD
segment (although, since it is part of a TG, it might be more likely IBD).
The size of the portions of segments that don't overlap should not be
considered when declaring a TG. (Although, presumably they could represent
differing portions of a longer segment (that you have) from the common
ancestor.)
[From all of the segments in a TG, you can make some calculations:
1. The size (use Mbp) of the overlap - although I have some TGs that are so
overlapping, that the "first one" and the "last one" don't overlap at all
2. You can calculate the segment you got from the Common Ancestor - Start of
the "first" shared segment with you to End of "last" shared segment with
you]
3. If you can view the segments the Matches in the TG share with each
other (at FI:A or GEDmatch), you can calculate the total segment that the
Common Ancestor had to have, that was passed down the various lines of
descent to the various Matches]
[I like to envision two long rows of bricks. The whole row is a chromosome;
the bricks (would need to be of various sizes) are the segments from
different ancestors; and the two rows are from your two parents. When you
form TGs, you are forming the bricks for both rows. So the TGs from one
chromosome, will not overlap each other, and may have varying gaps between
them, until you find enough Match/segments to define the whole brick
(segment from an ancestor)]
I would appreciate some feedback on this before I make a fool of myself in
my slide show!

[Hope this helps - jvb]
Thanks!
Don


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