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I'm trying to get my head round the correct GWAS terminology. I keep seeing the terms like "tag", "lead" and "index" SNP to be used almost interchangeably and I would like to get a clarification from someone inside the field.

My (limited) understanding is as follows: Tag SNP - the SNP included on the genotyping microarray. Once we have a compendium of SNPs for a given sample we can use reference haplotypes to impute the rest of the SNPs. Lead SNP = Index SNP - the SNP assigned the highest association significance after we've run association analysis for all the imputed SNP. The other SNPs in high LD with the lead SNP will form the associated locus.

Am I correct in my understanding? Any other / better terms I should be aware of?

Many thanks!

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  • $\begingroup$ Hi. One question for clarification: have you read the wikipedia article on "Tag SNP"? $\endgroup$ – Eff May 31 '18 at 10:59
  • $\begingroup$ I did. It explains "Tag SNP" quite clearly, but it doesn't really touch on "downstream" terminology, even in the GWAS section. Thanks for bringing it up though - it's a useful link to have in this question. $\endgroup$ – Ophiothrix Jun 5 '18 at 12:47
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I found a review paper that addresses your questions, see

Schaid, Chen, Larson (2018): From genome-wide associations to candidate causal variants by statistical fine-mapping

Tag SNP. You correctly identified tag SNPs. From the paper:

[T]he SNPs on microarrays, called tag SNPs...

Lead and index SNP. These are apparantly synonyms. From the paper:

This allows one to focus on the SNPs with the smallest (that is, most significant) P values in distinct regions, sometimes called the lead or index SNPs.

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