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Thread: Chromosome 6, HLAs, Ethnicity

  1. #1
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    Chromosome 6, HLAs, Ethnicity

    What causes a huge chunk of chromosome 6 to be inherited from only one parent? I was doing one-to-one comparisons on GEDmatch and noticed that this is the only location where a significant "block" was inherited from one parent. It looks like the same locations. I got the "block" from my father and my brother got the "block" from my mother.

    Is this just coincidence? Is it HLA related? I know my brother and I have different HLAs. Mine is found often in Siberia and Native Americans but in 3-5% frequencies in W Europe. Is it a coincidence that my father and I both show exactly 3% Finnish and my brother shows 0%?

    How many SNPs are the HLA types? I know HLA-DRB are "minor" ones but useful for grouping. How about the main HLA types of A,B,C?

    Me vs Father
    Chr6m2d.jpg

    Me vs Mother
    Chr6m2m.jpg

    Brother vs Father
    Chr6b2d.jpg

    Brother vs Mother
    Chr6b2m.jpg
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  2. #2
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    I don't understand what you mean. We inherit one chromosome 6 from each parent, including a copy of the HLA gene. However you only inherit each gene (or segment of gene, as they occasionally get split in two during meiosis) from only one grandparent on each parent's side. So you might have inherited one copy of your HLA gene from your maternal grandfather and the other your paternal grandmother, for example.

    Btw, I moved your thread as there is a subforum dedicated to HLA discussions (although I wonder if anybody noticed as it doesn't seem to generate much interest, despite it being at least as interesting as Y-DNA and mtDNA). If you browse this subforum, you'll see that I created distribution maps and explained the health associations for numerous HLA types. I also computed frequency tables for HLA-A and HLA-DR.

    I also made a list of HLA-DR SNPs. For others try looking on SNPedia.
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  3. #3
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    Thanks, Maciamo. Do you know how many total SNPs make up the HLAs?

    Can those affect ethnicity calculators?

    Are the green blocks in the pics a coincidence?

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  4. #4
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    There are thousands of SNPs. Here is a sample here.

  5. #5
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    I modified my Ancestry data file to set all chromosome 6 values to zero and uploaded to GEDmatch. It didn't affect it much, on a few calculators it pulled one percentage point or so from a Caucasian or West Asian into a Mediterranean or West European.

    The companies use HLA SNPs for ethnicity testing but it doesn't have a large effect on the results.

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