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  #1  
Old 1st March 2018, 09:03 AM
EricDu EricDu is offline
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Most shared segments are in same region of chromosome 22. Is that normal?

Looking at chromosome browser, I noticed that the same region of chromosome 22 consistently lit up. I exported the match data an viewed it in ADNA utility. With the default setting of 5cM, roughly two thirds of matched segments are on chromosome 22. When I increased the size to 7cM, the proportion increases to 85%.
Is this typical, or is it representative of a problem in the data?
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Old 1st March 2018, 11:40 AM
Ann Turner Ann Turner is offline
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There are some chromosomal regions that match more often than "expected." The table in the ISOGG Wiki has a list. C22 from ~ 16 to 25 Mb is one of these regions. Is that where your matches are found?

https://isogg.org/wiki/Identical_by_...ss_IBD_sharing

People may also have their own personal pile-ups.
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Old 2nd March 2018, 09:34 AM
John McCoy John McCoy is offline
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The situation in this part of chromosome 22 is messy, at best. I have some real matches in that area that triangulate in all combinations with each other, and in some cases extend farther to the left, thus very likely "real". The well-behaved matches happen to be paternal.

But there are at least an equal number of "matches" within the problem region that don't match with a large number of the other supposed members of the triangulation group, and they don't fall into a "maternal" group either. Rather, they match one or two of the others, more or less at random, and when I relax the matching criteria (in GEDmatch) for these problem kits, they still don't fall into distinct groups. I strongly suspect a lack of genetic diversity within this range, or else unusually poor data quality, structural heterogeneity, so some similar feature that causes the matching algorithm to misbehave. Sure wish somebody with access to a large number of raw data files that show these problems, and to a realistic approximation of the matching algorithms, could undertake a systematic analysis of this problem.
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Old 2nd March 2018, 01:20 PM
EricDu EricDu is offline
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Quote:
Originally Posted by Ann Turner View Post
There are some chromosomal regions that match more often than "expected." The table in the ISOGG Wiki has a list. C22 from ~ 16 to 25 Mb is one of these regions. Is that where your matches are found?
The matching segments are in the 36 to 42 region. See attached screenshot.
Attached Images
File Type: png Trevor-common-chr22.png (3.1 KB, 7 views)
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  #5  
Old 2nd March 2018, 03:01 PM
John McCoy John McCoy is offline
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Could well be a group of "real" matches! However, that doesn't automatically translate to "and I know who the common ancestor was" -- if the matches all involve just a single segment, the common ancestor would easily be too far back to identify with any certainty. It would be useful to see if they match in all combinations on GEDmatch, and it wouldn't be surprising if at least some of them are already on (free!) GEDmatch.

At least for me, the matches in that area (36M to 42M covers about 10 cM) have been well-behaved -- and easily sorted into two triangulation groups, one paternal, the other maternal. One group was identified as maternal because it included a known Reedy family (matching on other segments as well), the other group occupying the same chromosomal real estate that doesn't match with it must therefore be paternal.
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