Her identity by descent made flesh

By Razib Khan | April 29, 2012 2:49 pm

As I have indicated before, my daughter has a family tree where everyone out to 0.25 coefficient of relatedness has been genotyped by 23andMe. This is convenient in many ways. Before, relatedness was a theory. Now relatedness can be ascertained on the genomic level. Sometimes this can lead to peculiar consequences. “On paper” my daughter is 1/8 Scandinavian. Or 12.5%. But truly the expected value is 13.5%! (weighting by contributions from each maternal grandparent). Still, this remains an expected value. I would need a large sample of Scandinavians from that locale to make a truly precise guess as to the genetic contribution. Similarly, though I come in at about ~15 percent East Asian, my daughter looks to be a bit more East Asian than you’d expect based on that value (i.e., closer to 8-8.5 percent; I run her genotype more than a dozen times now). This may be a bias in the methodology, or, more likely it is simply the sampling error from my genome (I contributed more East Asian segments in the chromosomes passed down).

In any case, 23andMe has a “family inheritance” feature which is very convenient. It illustrates visually chromosome by chromosome the extent to which two individuals match genomic segments. Presumably this is useful for those who are distant cousins, who may match on a segment here and there. Instead of just focusing on one base pair, A/C/G/T, the method looks at the correlations of bases across a sequence of the chromosome. Below are the visualizations for matches of each individual with my daughter, in sequence: father, mother, paternal grandfather, paternal grandmother, maternal grandfather, maternal grandmother, paternal uncle, paternal uncle, paternal aunt, and maternal uncle. And no, I don’t know why it has an XY in the plots. For those of you without a biological background I hope that this can help in getting across how Mendelism manifests in a concrete manner. And if you do have a biological background, you can infer from these matches other interesting information about the meiotic process.


CATEGORIZED UNDER: Genetics, Genomics, Personal Genomics
MORE ABOUT: Personal genomics
  • Elizabeth

    That is so cool. It makes me wish I were still teaching a genetics course so that I could talk about these images with my students.

  • Dm

    Isn’t it unusual that she has an X-chromosome which is 100% from the mgm and 0% from the mgp? This thing is over 200cM in size yet must have had zero recombinations in the meiosis which led to the lucky oocyte?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #2, hm. i wonder if that alone might be responsible for why she’s more genetically derived from her maternal grandmother than grandfather….

  • Isabel

    This is super cool.
    I’m surprised there is not more variance in the relatedness to aunts and uncles, if I am reading it right. It has always fascinated me that while we are 50% identical to our parents, this is only true on average with siblings, and in fact it would seem unusual to end up right on 50% and then with another average she still ends up right around 25% with each it looks like. Hmm.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #4, you are correct. she is very close to her aunts/uncles to expected value. but varies more with her grandparents (0.22 to 0.28). also, you might be curious to know that two of my siblings are 0.41.

  • Eurologist

    And no, I don’t know why it has an XY in the plots.

    It’s probably just generic software for both genders. It does say “Not enough information” ;)

    As to the X chromosome, I wonder if the process/ software can even distinguish between two of them, or just simply assigns two 100% matches to the two plots of single Xs, each.

    Also, where could these have recombined? Aren’t they expected to stay intact?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    It’s probably just generic software for both genders.

    yeah. i assume the labor hours weren’t worth it. most people are OK with just autosome.

    Also, where could these have recombined

    females have two copies. one from mom, one from dad. so these can recombine. the male’s can not.

    i think the algorithm wasn’t performed on the x though.

  • Eurologist

    females have two copies. one from mom, one from dad. so these can recombine. the male’s can not.

    Yes, of course. I guess some of my brain cells temporarily switched to extreme male Chauvinism.

  • Dm

    23′s algorithm takes Xs and even makes specific corrections for sexes of the compared humans (like her matching blocks length threshold would have to be longer for matches with other females). But accounting for possible number of recombinations in regular English terms of relationship is next to impossible. The algorithm would have to infer how many female and male links are in the graph.

    I think that the Xs are really cool for historic genealogy, because the question of the direction of inheritance doesn’t exist for the male ancestors, and so even relatively less informative ethnic marks on the X should be easier to put in the proper historic and genealogical context. Alas, 23andMe doesn’t use HGDP data in its Ancestry Labs, and popular chromosome-painting utilities such as DYIDodecad don’t even look at the X at all.

    BTW with so many nodes on your pedigree, you should be able to phase genotypes and to map recombinations quite well?

  • Douglas Knight

    What is the normal rate of crossover? It looks to me like you have a rate of about once per chromosome. Is that correct? Or is it an artifact of the limited data? But the mother appears to have twice that rate. Is that the normal variation between instances of meiosis? between people?

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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