Recently, there was a paper Identification of Close Relatives in the HUGO Pan-Asian SNP Database by Xiong Yang, Shuhua Xu, and the HUGO Pan-Asian SNP Consortium.
three individuals involved in MZ pairs were excluded from the whole dataset to construct standardized subset PASNP1716; seventy-six individuals involved in first-degree relationships were excluded from PASNP1716 to construct standardized subset PASNP1640; and 57 individuals involved in second-degree relationships were excluded from PASNP1640 to construct standardized subset PASNP1583. The individuals excluded were summarized in Table S6, S7, S8.
Let me engage in some blog triumphalism by saying I wrote about the duplicates and relatives in the Pan-Asian dataset in April 2011.
Here are my blog posts about relatedness in datasets:
- HapMap related samples
- Behar related samples
- Xing related individuals
- Henn 2011 duplicates
- Rasmussen relatives
- Austroasiatic samples
- Pan-Asian relatives
- Latino relatives
- 1000genomes related samples
- Reich duplicates
- Metspalu related samples
Early on, I was removing only first degree relatives from the reference datasets. Nowadays, I try to remove all second degree relatives too. I leave the third degree relatives in the data since it's sometimes hard to figure out how real the low IBD values are in Plink. There are a lot of 3rd degree relatives if Plink is to be believed, but I am a little skeptical.
Since Plink's IBD analysis requires homogenous samples, I am now using KING (paper) for the purpose. I am also looking at kcoeff (paper)
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