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JAX
2012-10-29, 00:37
I was wondering if anyone could possibly help me with this? On chromosome 22 I have a segment that looks like it could be a true ancient Siberian/North Eurasian segment. Dr. McDonald's test picked it up and I can see that on GEDmatch using the ADMIXTURE proportions by chromosome tool I score pretty high in most analysis in Siberian/North Eurasian on chromosome 22. I know that I inherited this segment from my father as he also has this segment in his McDonald analysis and his chromosome 22 results form GEDmatch also show high Siberian/North Eurasian scores. It seems also that ultimately I inherited this segment from my paternal grandmother who was of Finnish descent as my paternal grandfather who has tested with 23andme does not have this segment in his own DNA at all. Here is the segment I am examining below on my Dr. McDonald results and also a few of my chromosome 22 scores from GEDmatch.

http://imageshack.us/a/img580/1696/jacksondevonifull201208.png

GEDmatch Eurogenes K9 Chromosome 22: Siberian=14.3%

GEDmatch Eurogenes K13 Chromosome 22: North Eurasian=15.9%

GEDmatch Dodecad K12b Chromosome 22: Siberian=15.5%


So I am wondering then is there any way that I can confirm if these results are real? I mean do they actually represent true Siberian/North Eurasian ancestry in my genome even if it is ancient?

muso
2012-10-29, 00:40
Gedmatch has an option, "show results that match on a given chromosome segment." Have you tried to enter the segment portions and see who comes up?

jibarodepr
2012-10-29, 00:59
You also have Amerindian in chromosome 4

amerinese
2012-10-29, 01:23
I don't know what else you could do to confirm, beyond what you have already done, other than to find an actual Siberian who you share that segment with. You could run the Gedmatch option that Muso suggested. Assuming there isn't a match out there for that segment on Gedmatch or 23andMe etc. that leaves you without any further options.

jibarodepr
2012-10-29, 01:31
MDLP World 22 can help you on it

JAX
2012-10-29, 01:42
Gedmatch has an option, "show results that match on a given chromosome segment." Have you tried to enter the segment portions and see who comes up?

Thank you muso I will definitely check that out and see if anything turns up.

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You also have Amerindian in chromosome 4

Yes I noticed that as well but the strange thing there is that both my father and mother have no Amerindian segment in that location on chromosome 4. This segment also showed up when Polako did some chromosome paintings for us a little while back. Maybe it is just noise?

jibarodepr
2012-10-29, 01:44
Yes I noticed that as well but the strange thing there is that both my father and mother have no Amerindian segment in that location on chromosome 4. This segment also showed up when Polako did some chromosome paintings for us a little while back. Maybe it is just noise?I think so.

JAX
2012-10-29, 01:44
MDLP World 22 can help you on it

I have run my results with MDLP World 22. The thing here is that my Siberian/North Eurasian results seem to disappear in that analysis. It may be that they got absorbed into the North-European-Mesolithic component in that analysis.

jibarodepr
2012-10-29, 01:47
I have run my results with MDLP World 22. The thing here is that my Siberian/North Eurasian results seem to disappear in that analysis. It may be that they got absorbed into the North-European-Mesolithic component in that analysis.Then that means your "Asian" is truly Eastern European input

JAX
2012-10-29, 01:53
Then that means your "Asian" is truly Eastern European input

I thought that the North-European-Mesolithic component has some ''Asian'' type make up to it? Or at least affinities to the ''Asian'' components.

jibarodepr
2012-10-29, 01:56
I thought that the North-European-Mesolithic component has some ''Asian'' type make up to it? Or at least affinities to the ''Asian'' components.yes, it has affinity, but it is not "Asian" per se, but more similar to Amerindian

JAX
2012-10-29, 02:10
yes, it has affinity, but it is not "Asian" per se, but more similar to Amerindian

Hmmm well here are my component scores for chromosome 22 for the MDLP World 22 analysis.

West Asian: 20.9%
North-European-Mesolithic: 12.2%
North Siberian: 4.8%
Atlantic-Mediterranean-Neolithic: 21.0%
Samoedic: 0.8%
North-East-European: 34.7%
South-African: 0.7%
Melanesian: 4.9%

So from the looks of this it looks like my Siberian/North Eurasian scores from other analysis may have been absorbed into various other components such as the North-European-Mesolithic one.

jibarodepr
2012-10-29, 02:24
Hmmm well here are my component scores for chromosome 22 for the MDLP World 22 analysis.

West Asian: 20.9%
North-European-Mesolithic: 12.2%
North Siberian: 4.8%
Atlantic-Mediterranean-Neolithic: 21.0%
Samoedic: 0.8%
North-East-European: 34.7%
South-African: 0.7%
Melanesian: 4.9%

So from the looks of this it looks like my Siberian/North Eurasian scores from other analysis may have been absorbed into various other components such as the North-European-Mesolithic one.I see you scored North Siberian also

JAX
2012-10-29, 02:34
^Yes I do a little bit. Maybe my Siberian/North Eurasian got absorbed partially into the North-European-Mesolithic component and some also went into North Siberian. Hard to say really I think.

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Gedmatch has an option, "show results that match on a given chromosome segment." Have you tried to enter the segment portions and see who comes up?

Sorry for being stupid here but how do I locate the exact location of this particular segment? How do I find it's start and ending locations?

muso
2012-10-29, 10:25
Sorry for being stupid here but how do I locate the exact location of this particular segment? How do I find it's start and ending locations?

Well, if you look at the graph Dr. McDonald provided, you will see a series of measurements at the bottom of the graph. Looking at the picture you provided in this thread, it looks like the Asian segment is from about 25000000 to about 31000000. You can zoom in on the graph and get a better read. When you input the information into Gedmatch I believe you need to leave out the commas; just put in the numerals.

JAX
2012-10-29, 10:46
^Great thanks man!

muso
2012-10-29, 10:50
Let us know what you find.

yahooland
2012-10-29, 11:05
I have a suspicious black segment at chromosome 16: i got 7% sub saharan on eurogene and 5,5 on MDLP22. it's that noise ?

JAX
2012-10-29, 11:07
Okay when I put in 25000000 to about 31000000 in GEDmatch I get a number of matches there. My father and mother of course both show up and so does my brother. Here are my matches with non-direct family members.

23,980,406-28,411,588 for 11.8 cM on 1,516 SNPs. (Alli Kivineva) (Finnish)

23.949,339-25,862,474 for 7.0 cM on 1,054 SNPs. (Enya)

24,788,134-28,441,558 for 9.3 cM on 1,256 SNPs. (Antti Poro) (Finnish)

25,852,430-29,883,510 for 6.0 cM on 1,466 SNPs. (Pavel Reutov) (Russian)

I do not know what Enya's ethnicity is but the rest of my matches here appear to be either Finnish or Russian from the looks of their names.

muso
2012-10-29, 20:18
Okay when I put in 25000000 to about 31000000 in GEDmatch I get a number of matches there. My father and mother of course both show up and so does my brother. Here are my matches with non-direct family members.

23,980,406-28,411,588 for 11.8 cM on 1,516 SNPs. (Alli Kivineva) (Finnish)

23.949,339-25,862,474 for 7.0 cM on 1,054 SNPs. (Enya)

24,788,134-28,441,558 for 9.3 cM on 1,256 SNPs. (Antti Poro) (Finnish)

25,852,430-29,883,510 for 6.0 cM on 1,466 SNPs. (Pavel Reutov) (Russian)

I do not know what Enya's ethnicity is but the rest of my matches here appear to be either Finnish or Russian from the looks of their names.
Well I am no expert, but those results seem reasonable and consistent with your readings on this segment. Maybe the Siberian goes back to the Finnish? I know we have plenty of Finnish members who could probably lend some insight.

uncut
2012-10-29, 22:11
So I am wondering then is there any way that I can confirm if these results are real? I mean do they actually represent true Siberian/North Eurasian ancestry in my genome even if it is ancient?
Can you get something out of SupportMix (e.g. Chr22.zip\Chr22\EU11\outSupportMix.png)?
The large Evenk_Yakut found there should be some East Asian stuff (if you are CA1).

There are some useful instructions and info under "Update 2".
http://bga101.blogspot.se/2012/07/pinpointing-loci-specific-genomic.html

I tried to check a segment on one of my chromosomes this way.
From what I have understood, you can find out if it is "uncertain" or "decent probability".

JAX
2012-10-30, 02:43
^Yes you are correct that on SupportMIX I show a large Evenk_Yakut segment on chromosome 22. This seems to match my McDonald and other results. Also I have found a Nganassan segment match on chromosome 22 from the fastIBD that Polako also did for us a little while back. I do not know if this segment is in the exact same location as this ''Asian'' segment that we are discussing here or not though.

uncut
2012-10-30, 06:52
^Yes you are correct that on SupportMIX I show a large Evenk_Yakut segment on chromosome 22. This seems to match my McDonald and other results. Also I have found a Nganassan segment match on chromosome 22 from the fastIBD that Polako also did for us a little while back. I do not know if this segment is in the exact same location as this ''Asian'' segment that we are discussing here or not though.Yes they are different, not least because they are in pairs (a, b).

Trinkar
2012-11-14, 01:07
In my X-Chromosone i have around 9% south Asian and 91% european ( no other mix)

In my chromosones numbers 6 and 8 only,.... I have about 20% of the lower bar showing middle-east , and every other chromomosone has 100% european.
I was wondering, if the lower bar represents the maternal or paternal of a person