次要等位基因频率匹配? [英] Minor allele frequency matching?

问题描述

我有一个SNP列表，我已经从1000个基因组试点1中获得了MAF和LD的代理SNP.我想知道当每个人都提到MAF匹配时，它们是否需要完全相同?

I have a list of SNPs that I have already obtained their proxy SNPs with MAF and LD from 1000 genomes pilot 1. I want to know when everybody mentions about MAF matching, do they need to be exactly the same?

例如，感兴趣的SNP的MAF为0.35，如果代理SNP的MAF为0.37，是否可以用作良好的代理?给定两个> 0.8

For example, the SNP of interest has MAF 0.35, if the proxy SNP has MAF 0.37, can it be used as a good proxy? Given LD of the two >0.8

是否绝对必须选择MAF等于0.35的代理?

Do have absolutely have to choose a proxy that has a MAF equals 0.35?

推荐答案

LD取决于MAF，即高R平方表示MAF相似.参见:

LD as measured by R-sq is dependent on MAF ie high R-squared implies MAFs are similar. See:

https://www.ncbi.nlm.nih.gov/pubmed/18572214

因此，非常高的R平方通常意味着SNP之间的MAF相似.

So, very high R-squared usually means MAF between the SNPs are similar.

此外，代理SNP的选择通常仅取决于LD度量.如前所述，MAF已合并"到计算中，因此不需要进行匹配.如果您有多个具有相同LD的代理，请选择一个具有最相似MAF的代理.

Also, selection of proxy SNPs is typically dependent on LD measure only. As mentioned MAF is "incorporated" into the calculation, so matching for it is not necessary. If you have multiple proxies with same LD, then choose one with most similar MAF.

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