名词解释 | Lead SNPs | credible SNPs | Polygenicity | Discoverability

GWAS catalog里面的snp可以称作reported SNP

 

lead SNPs 就是曼哈顿图里每根柱子最顶上的那个SNP

考虑LD的话，就是从每个loci 里面，选出P最小的点

 

Lead SNPs做了fine mapping后就得到了causal SNPs，即credible SNPs。

Lead SNPs (that is, defined by LD and P values) are not necessarily the causal SNPs in trait-associated loci24.

We, therefore, performed fine mapping using FINEMAP25 for 41,041 trait-associated loci from 466 traits to obtain credible SNPs and characterized these in the same way as was done for lead SNPs (see Methods, Supplementary Note and Supplementary Fig. 11).

 

Polygenicity and discoverability of traits

Estimating the polygenicity (proportion of causally associated single nucleotide polymorphisms (SNPs)) and discoverability (effect size variance) of causal SNPs for human traits is currently of considerable interest.

Estimates of polygenicity and discoverability allow one to estimate compound quantities, like narrow-sense heritability captured by the SNPs [17]; to predict the power of larger-scale GWAS to discover genome-wide significant loci; and to understand why some phenotypes have higher power for SNP discovery and proportion of heritability explained than other phenotypes.

 

参考：

Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model