Boudin
12-19-2023, 04:15 AM
I've been experimenting running K36 on specific segments of my DNA believed to descend from a common ancestor, in the hopes of verifying the ethnicity of this long-dead individual. From a different thread:
The solution, I've recently learned, is to modify only the chromosome containing the segment of interest in the 23andMe file. Delete all rows for that chromosome except those containing the segment, then make each row homozygous for the segment's chromosome. So if the segment is on copy 2, and the genotype is AC, make the genotype CC instead.
Then upload the file to GEDmatch for research purposes, and you can immediately run K36 on each chromosome. Of course you are only interested in the results for the chromosome containing the segment of interest.
I've applied this technique to segments labeled "Indigenous American" by 23andMe in my own, and others', DNA. Here are the coordinates:
BoudinSegmentChr2,19.2,0,0,0,0,0,0,0,0,0,0,0,0,0,0 ,0,0,0,0,0,0,0,6.2,0,0,0,0,0,0,0,0,0,74.7,0,0,0
BoudinSegmentChr12,0,0,0,0,0,0,0,0,0,0,0,0,0,64,0, 0,0,0,26,0,0,0,0,0,0,2.1,0,0,0,0,7.8,0,0,0,0,0
BoudinSegmentChr14,30.5,0,0,0,0,24.1,0,0,0,0,11.8, 0,0,0,0,0,0,0,6.8,0,0,0,0,0,0,0,0,0,17.6,9.1,0,0,0 ,0,0,0
BoudinSegmentChr16,44.3,0,0,0,0,0,0,0,0,0,0,0,55.7 ,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Cajun1SegmentA,24.6,0,21.2,0,0,0,0,0,0,0,0,0,14.9, 9.2,0,0,0,0,0,0,8.2,0,8.2,0,0,0,0,0,0,0,0,0,0,0,0, 3
Cajun1SegmentB,0,0,0,2.8,0,28.7,0,0,0,0,0,0,0,0,0, 0,10.7,0,0,0,0,0,0,0,0,18,0,0,42.6,0,0,0,0,0,7.9,0
Cajun1SegmentC,52.2,0,7.8,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,29.3,0,0,0,0,0,0,0
Cajun1SegmentD,52.6,0,0,0,0,0,0,0,17.9,0,0,0,0,0,0 ,0,0,0,15.8,0,0,0,0,1.4,0,0,0,0,0,12.3,0,0,0,0,0,0
Cajun2SegmentA,35.2,0,0,0,0,0,0,0,0,0,0,0,0,46.9,0 ,0,0,0,0,0,0,0,0,0,0,14.7,0,0,3.2,0,0,0,0,0,0,0
Cajun2SegmentB,41.7,27.3,0,20.3,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,3.8,0,0,0,0,0,0,6.9,0,0,0,0,0,0,0
Cajun2SegmentC,28.8,0,0,2.6,0,13.4,0,0,0,0,0,0,22. 6,0,0,0,0,0,0,0,7.5,8.6,0,0,0,0,0,0,16.6,0,0,0,5.8 ,0,0,0
Here are the shortest distances, using these sources (https://www.theapricity.com/forum/showthread.php?320239-Eurogenes-K36-On-Vahaduo):
Mari
Finnish_SW
Mixed_Inuit
Sioux_SouthDakota
Costa_Rica
Shor
Sioux_SouthDakota
Sioux_SouthDakota
Saami_NO
Mexican_Mestizo
Mixed_Inuit
9 of 11 are Arctic populations, and the most common one, Sioux_SouthDakota, is consistent with the "Great Lakes & Canada" region assigned to a close relative's 1% Amerind (not used in this analysis).
This is fantastic, in my opinion, and apparently this is exactly what the creator intended K36 for (https://bga101.blogspot.com/2013/03/eurogenes-k36-at-gedmatch.html):
The main purpose of the Eurogenes K36 is to help users unravel the ethnic origins of local areas of their genomes (aka. half-segments), hence the high number of ancestral categories, some of which are very specific. In other words, the test is mainly a chromosome painting utility.
The solution, I've recently learned, is to modify only the chromosome containing the segment of interest in the 23andMe file. Delete all rows for that chromosome except those containing the segment, then make each row homozygous for the segment's chromosome. So if the segment is on copy 2, and the genotype is AC, make the genotype CC instead.
Then upload the file to GEDmatch for research purposes, and you can immediately run K36 on each chromosome. Of course you are only interested in the results for the chromosome containing the segment of interest.
I've applied this technique to segments labeled "Indigenous American" by 23andMe in my own, and others', DNA. Here are the coordinates:
BoudinSegmentChr2,19.2,0,0,0,0,0,0,0,0,0,0,0,0,0,0 ,0,0,0,0,0,0,0,6.2,0,0,0,0,0,0,0,0,0,74.7,0,0,0
BoudinSegmentChr12,0,0,0,0,0,0,0,0,0,0,0,0,0,64,0, 0,0,0,26,0,0,0,0,0,0,2.1,0,0,0,0,7.8,0,0,0,0,0
BoudinSegmentChr14,30.5,0,0,0,0,24.1,0,0,0,0,11.8, 0,0,0,0,0,0,0,6.8,0,0,0,0,0,0,0,0,0,17.6,9.1,0,0,0 ,0,0,0
BoudinSegmentChr16,44.3,0,0,0,0,0,0,0,0,0,0,0,55.7 ,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Cajun1SegmentA,24.6,0,21.2,0,0,0,0,0,0,0,0,0,14.9, 9.2,0,0,0,0,0,0,8.2,0,8.2,0,0,0,0,0,0,0,0,0,0,0,0, 3
Cajun1SegmentB,0,0,0,2.8,0,28.7,0,0,0,0,0,0,0,0,0, 0,10.7,0,0,0,0,0,0,0,0,18,0,0,42.6,0,0,0,0,0,7.9,0
Cajun1SegmentC,52.2,0,7.8,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,29.3,0,0,0,0,0,0,0
Cajun1SegmentD,52.6,0,0,0,0,0,0,0,17.9,0,0,0,0,0,0 ,0,0,0,15.8,0,0,0,0,1.4,0,0,0,0,0,12.3,0,0,0,0,0,0
Cajun2SegmentA,35.2,0,0,0,0,0,0,0,0,0,0,0,0,46.9,0 ,0,0,0,0,0,0,0,0,0,0,14.7,0,0,3.2,0,0,0,0,0,0,0
Cajun2SegmentB,41.7,27.3,0,20.3,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,3.8,0,0,0,0,0,0,6.9,0,0,0,0,0,0,0
Cajun2SegmentC,28.8,0,0,2.6,0,13.4,0,0,0,0,0,0,22. 6,0,0,0,0,0,0,0,7.5,8.6,0,0,0,0,0,0,16.6,0,0,0,5.8 ,0,0,0
Here are the shortest distances, using these sources (https://www.theapricity.com/forum/showthread.php?320239-Eurogenes-K36-On-Vahaduo):
Mari
Finnish_SW
Mixed_Inuit
Sioux_SouthDakota
Costa_Rica
Shor
Sioux_SouthDakota
Sioux_SouthDakota
Saami_NO
Mexican_Mestizo
Mixed_Inuit
9 of 11 are Arctic populations, and the most common one, Sioux_SouthDakota, is consistent with the "Great Lakes & Canada" region assigned to a close relative's 1% Amerind (not used in this analysis).
This is fantastic, in my opinion, and apparently this is exactly what the creator intended K36 for (https://bga101.blogspot.com/2013/03/eurogenes-k36-at-gedmatch.html):
The main purpose of the Eurogenes K36 is to help users unravel the ethnic origins of local areas of their genomes (aka. half-segments), hence the high number of ancestral categories, some of which are very specific. In other words, the test is mainly a chromosome painting utility.