A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs.
Yihan ZhaoDi WuDanli JiangXiaoyu ZhangTing WuJing CuiMin QianJean ZhaoSteffi OesterreichWei SunToren FinkelGang LiPublished in: Nature communications (2020)
GWAS cannot identify functional SNPs (fSNP) from disease-associated SNPs in linkage disequilibrium (LD). Here, we report developing three sequential methodologies including Reel-seq (Regulatory element-sequencing) to identify fSNPs in a high-throughput fashion, SDCP-MS (SNP-specific DNA competition pulldown-mass spectrometry) to identify fSNP-bound proteins and AIDP-Wb (allele-imbalanced DNA pulldown-Western blot) to detect allele-specific protein:fSNP binding. We first apply Reel-seq to screen a library containing 4316 breast cancer-associated SNPs and identify 521 candidate fSNPs. As proof of principle, we verify candidate fSNPs on three well-characterized loci: FGFR2, MAP3K1 and BABAM1. Next, using SDCP-MS and AIDP-Wb, we rapidly identify multiple regulatory factors that specifically bind in an allele-imbalanced manner to the fSNPs on the FGFR2 locus. We finally demonstrate that the factors identified by SDCP-MS can regulate risk gene expression. These data suggest that the sequential application of Reel-seq, SDCP-MS, and AIDP-Wb can greatly help to translate large sets of GWAS data into biologically relevant information.
Keyphrases
- genome wide
- mass spectrometry
- dna methylation
- high throughput
- gene expression
- ms ms
- multiple sclerosis
- liquid chromatography
- single cell
- circulating tumor
- gas chromatography
- high performance liquid chromatography
- capillary electrophoresis
- high resolution
- cell free
- single molecule
- transcription factor
- electronic health record
- big data
- genome wide association study
- south africa
- protein protein
- small molecule
- dna binding
- amino acid
- circulating tumor cells
- healthcare
- human immunodeficiency virus
- hepatitis c virus
- young adults
- tandem mass spectrometry
- social media
- high throughput sequencing