SNPs-seq

Overview

SNPs-seq (also referred to as SNP-seq or high-throughput allele-specific protein-binding assay) is a functional genomics screening method that measures allele-specific protein binding across large numbers of SNP loci simultaneously. The method uses a competitive binding approach: paired oligonucleotides carrying the reference and alternate alleles of candidate SNPs are incubated with nuclear extracts, and differential protein binding is quantified by sequencing (giving a “biased allelic binding” or BAB score). This enables systematic prioritization of GWAS risk loci to identify the functional causal variant(s) driving disease association.

Used by

• Applied to 374 prostate-cancer GWAS risk loci in the NOL10/USF1 prostate cancer study; identified rs4519489 (NOL10 intron, 2p25 locus) as exhibiting strong biased allelic binding with the risk A allele binding more protein than the T allele, leading to its nomination as the functional causal SNP PMID:28927585

Notes

• Scales to hundreds or thousands of loci in a single experiment, outperforming traditional one-locus-at-a-time EMSA for GWAS functional prioritization.
• BAB scores are agnostic to identity of the binding protein; downstream ChIP-seq, EMSA, and proteomics are needed to identify specific TF binders.
• Corpus-grown slug; not registered as a canonical assay type in cBioPortal.

Sources

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