Neandertal (haplotype) in the family!

There is pretty much a 100% probability that I carry Neandertal origin genes, since I’m Eurasian. That being said, I hadn’t looked too closely into the matter in regards to my own genome, because the whole “which SNPs are Neandertal” issue has been pretty dicey. But after the “Neandertal dystrophin” paper sniffing for whether you carry a specific Neandertal haplotype got a whole lot easier. The authors provided the markers and their associated haplotypes within the paper. So if the B006 haplotye is Neandertal, by looking at your markers in 23andMe through the browse raw data feature you can figure out what your lineage is, and see if you are indeed “Neandertal” on that locus. Since it’s on the X chromosome, males will carry only one copy of the gene. On the other hand, if you’re a woman you’ll have two copies, so ascertaining what specific combination of markers you have spanning a particular genomic segment can be more difficult (the results are not “phased,” so you don’t know if the allele is from the mother or father on any given genotype). But inferring the sequence of markers on a strand of DNA is much easier if you have relatives to compare with.

As you know the results for my first sibling came back earlier this week. I decided to look at which haplotypes we carried. Below the fold are the SNPs (the links will take you to 23andMe, so if you are logged into your account it will take you to where you need to go):

Here the SNPs in the 23andMe data base (one will be missing for v2) :

rs1456740
rs6628685
rs331370
rs2854965
rs6653863
rs331369
rs331368
rs331367
rs331366

Record the genotype. I found it convenient to enter them into a spread sheet if there were two copies for an individual, since you’ll have to engage in elimination of possibilities by looking at the possible combinations.

Here are alleles:

B006 AATGAATTT  – Archaic or Neanderthal
B012 AATGAATTT  African ancient branch
B007 AATGAATCT  African ancient branch
B001 GACGGCTTG  World wide distribution
B002 AGTGAATTT  World wide distribution
B005 GATTGACCT  World wide distribution
B008 GACGGATCT  World wide distribution
B009 GACTGCTCG  World wide distribution
B003 GACTGCTTG  World wide distribution
B010 GATGAATCG  World wide distribution
B011 GATTGCCCG  World wide distribution
B004 GGTGAATTT  Non-African

And now percentages outside Africa rounded to the nearest digit (so if you are female and not African you can eliminate the Africa distinctive possibilities):

(note that the rounding means that some haplotypes with trace non-African proportions are now ~0)

So what did I find? I carry the most common non-African haplotype, B001. But here’s the interesting thing: I found that my sibling carries one copy of the B006 haplotype! So at least one of my parents has at least one copy of that haplotype. I find this particularly of interest because of dystrophin’s phenotypic consequences in terms of muscle development. I have one sibling whose results are going to come in soon who happens to resemble me a great deal physically…except for the fact that while I am gracile, they are robust. You can guess my amusement if it turns out that this sibling carries the Neandertal haplotype on this locus!

Note: Credit to Ted Kandell for the “leg work” in the 23andMe forums.