Question: Obtain genotype data from Eurasian and HapMap populations
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gravatar for rednalf
10 weeks ago by
rednalf20
rednalf20 wrote:

I have seen this figure in a Nature Immunology paper. I was wondering where I can find the genotype data from the 36 populations (32 Eurasian populations and 4 HapMap populations) in panel b. Do you know if it is open access? I couldn't find anything online.

Nature Immunology Figure

snp genome • 136 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by rednalf20

Sure, it is Supplementary Figure 21 of https://www.nature.com/articles/s41590-018-0049-7

ADD REPLYlink written 10 weeks ago by rednalf20

Thanks - you should check the supplementary information for the purposes of finding out where the data is actually stored. I imagine that it is controlled access.

By the way: one project that I failed to mention was Greater Middle East

ADD REPLYlink written 10 weeks ago by Kevin Blighe28k
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gravatar for Kevin Blighe
10 weeks ago by
Kevin Blighe28k
Republic of Ireland
Kevin Blighe28k wrote:

You can download and prepare the 1000 Genomes Phase III data by following my previous tutorial, here: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (note the PED file, which allows you to distinguish the populations). I frequently use this data for various diverse studies.

Regarding HapMap, the project is old and now retired. See the notice from the NCBI, Here. By following the links on that page, you should still be able to obtain the data, though.

Kevin

ADD COMMENTlink written 10 weeks ago by Kevin Blighe28k

Thank you Kevin for your answer. I have been doing PCAs using 1KG data (CEU, GIH, MEX, TSI, YRI, etc.) and your tutorial (thank you btw), but since my cohort is French I was interested in plotting my samples with cohorts with a more precise ancestry (only Eurasians) to see if they overlap with French individuals, as done in panel b in the figure here above.

ADD REPLYlink written 10 weeks ago by rednalf20

Can you paste the link to the publication?

ADD REPLYlink written 10 weeks ago by Kevin Blighe28k
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