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Archiver > GENEALOGY-DNA > 2008-05 > 1211914534


From: Anders Pålsen <>
Subject: [DNA] X-SNP male haploblocks useful?
Date: Tue, 27 May 2008 18:55:34 +0000 (GMT)


List,

I refined out most of the X-SNP markers from the 2 GIG 650K HGDP-CEPH 50+ population panel, totaling about 16K of X-SNP markers (all in deCODEme). I removed all the female samples and was left with 562 male samples that can be assumed to be phased, sorted them in correct ascending order in basepair distance between the markers and marker names. These again I compared to the reference sequence using a spreadsheet for all the 16k markers and all the 562 individuals. I made a system where 0 equals a match and 1 equals a dismatch. I then had material available to possibly find common or not common linked fragments compared to the reference sample.

The x-blocks imidatly appeared in the data for example the markers rs5925000, rs4330820, rs7050250 with only 6519 basepairs between first to third appears in great majority in all part of the world (including the reference sample), the mutations/recombinations that may have occured do not seem to isolate in any particular population or world region so it may be old stuff from Africa or the markers is to few making it identical by state.

Another observation I have noticed is when recombination or mutation have occured in a very closely linked haploblock not only a single marker changed but the whole block. A good example is the markers rs12388803, rs4969625, rs1105708, rs7888284, rs7886032, rs2211428, rs10521400, rs6522929 with a distance only 40361 basepairs. It appears in several cases that the whole block changed when there was a mutation or recombination event.

Anders




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