Journal Article

A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs

Sun, Wei, Finkel, Toren, Li, Gang, Qian, Min, Zhao, Yihan, Zhao, Jean, Jiang, Danli, Wu, Di, Zhang, Xiaoyu, Oesterreich, Steffi, Wu, Ting, Cui, Jing

2020

Overview

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. It is often difficult to identify functional SNPs from disease-associated SNPs in linkage disequilibrium. Here, the authors present Reel-seq, SDCP-MS and AIDP-Wb, three sequential methodologies for fSNP identification and characterization.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 49 / 49/47 / 631/208/205 / 631/208/205/2138 / 692/4028/67/1347 / Adaptor Proteins, Signal Transducing - genetics / Alleles / Blotting, Western / Breast cancer / Breast Neoplasms - genetics / Breast Neoplasms - pathology / Cell Line, Tumor / Deoxyribonucleic acid / DNA / DNA sequencing / Female / Fibroblast growth factor receptor 2 / Gene expression / Gene Expression Regulation, Neoplastic / Genetic Predisposition to Disease - genetics / Genome-Wide Association Study - methods / Humanities and Social Sciences / Humans / Linkage Disequilibrium / Loci / MAP Kinase Kinase Kinase 1 - genetics / Mass spectrometry / Mass Spectrometry - methods / Mass spectroscopy / MCF-7 Cells / multidisciplinary / Polymorphism, Single Nucleotide / Proteins / Receptor, Fibroblast Growth Factor, Type 2 - genetics / Regulatory Sequences, Nucleic Acid - genetics / Science / Science (multidisciplinary) / Sequence Analysis, DNA - methods / Single-nucleotide polymorphism