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closeReferee comments: Referee 1
Posted by PLOS_ONE_Group on 04 Jan 2008 at 14:30 GMT
Referee 1's review:
The paper submitted by David Serre and colleagues present a sequence of steps designed to limit the effect of population structure and hidden relationship in case-control association study with high degree of population structure.
The main drawback is the relatively small number of genotyped SNPs that prevent the authors from giving a dense genome-wide perspective: analysis such as STRUCTURE necessarily have a limited power with that number of SNPs.
However, I think the authors have done what was possible given the dataset. They show convincingly that the reduction in sample size generated by cleaning the dataset lowers the false positive rate but does not affect true associations.
I find the discussion interesting and I appreciate the comparison between EIGENSTRAT and STRUCTURE in this situation. I am curious to see what sort of principal components EIGENSTRAT would find with that dataset. What would be the equivalent of Fig 2 with EIGENSTRAT? (looking at the first three components I suppose).
Besides that small question (which is not essential for this study), I think this paper is ready for publication.
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N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.