"Eight of the 19 variants that were genome-wide significant (P < 5 × 10−8) in the discovery GWAS were not genome-wide significant in the combined analysis, consistent with small effect sizes and limited power but also with genetic heterogeneity."Is that really what it's consistent with? If you have variants that were found to be significant in previous studies and you include the data from those studies in your current study, even if the effect size was small (and, the power now increased), you should expect most of them to retain significance, even if they weren't significant in the new data set independently. The fact that half of them have lost significance is a good indication that most or all of them were false positives to begin with. Moreover, once again, why not do an independent GWAS (I'm assuming they did not) of the new data and compare it to the old data?
Now let's look at the very next sentence:
In the combined analysis, 30 loci were genome-wide significant, including 20 newly identified loci.So 10 (or 11, unclear) of the loci did not replicate out of 19, even with the datasets in which they were found significant, then 20 new loci are added. If these were again false positive, one would expect an increase in the number of false positives with additional data. What is the reason for assuming that these 20 novel loci are anything more than the next batch of false positives until the next meta-analysis comes along? This is yet another example of a GWAS study that folds over old data into a meta-analysis and makes no attempt to assess the new data independently, making it impossible to determine whether ANY of the previous loci were independently replicated.
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