Obtain genotype data from Eurasian and HapMap populations

Question

[rednalf]

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.

[rednalf]

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

[Kevin Blighe]

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

Answer 1

[Kevin Blighe]

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

[rednalf]

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.

[Kevin Blighe]

Can you paste the link to the publication?