The data sets in the dark

By Razib Khan | February 24, 2012 12:09 pm

Recently I was tipped off to the appearance of a new paper, Genome-Wide Association Study Identifies Chromosome 10q24.32 Variants Associated with Arsenic Metabolism and Toxicity Phenotypes in Bangladesh. This is the section which caught my eye: “Using data on urinary arsenic metabolite concentrations and approximately 300,000 genome-wide single nucleotide polymorphisms (SNPs) for 1,313 arsenic-exposed Bangladeshi individuals.” 300 K SNPs with 1,313 Bangladeshi individuals is a lot! I’m interested in this data set because of the 200+ participants in the Harappa Ancestry Project my parents remain the “unadmixed” South Asians with the highest fraction of East Asian ancestry (10-15 percent). Within South Asia aside from those groups with clear East Asian affinities only peoples of Munda background have the same levels. This data set could answer a lot of questions as to the typicality of my parents (literally within a few hours in terms of data exploration). But this is all you get in the supplements:

 


Zack Ajmal has already sent off an email asking about this data set, so hopefully the results will be positive.

This is a medical genetics study, so all they wanted to confirm is that there wasn’t population stratification due to inbreeding. They confirmed that. It is fine if they don’t want to explore further questions in relation to ancestry, but it would be really depressing if the data set can never see the light of day for those who are interested in asking other questions.

MORE ABOUT: Bangladesh
  • http://www.zackvision.com/weblog/ Zack

    That PCA plot was so disappointing!

  • pconroy

    That would be cool – as you might be able to infer Tibeto-Burman from Munda origins…

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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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