GERV: A Statistical Method for Generative Evaluation of Regulatory Variants for Transcription Factor Binding

BioRxiv : the Preprint Server for Biology
Haoyang ZengDavid K. Gifford

Abstract

The majority of disease-associated variants identified in genome-wide association studies (GWAS) reside in noncoding regions of the genome with regulatory roles. Thus being able to interpret the functional consequence of a variant is essential for identifying causal variants in the analysis of GWAS studies. We present GERV (Generative Evaluation of Regulatory Variants), a novel computational method for predicting regulatory variants that affect transcription factor binding. GERV learns a k-mer based generative model of transcription factor binding from ChIP-seq and DNase-seq data, and scores variants by computing the change of predicted ChIP-seq reads between the reference and alternate allele. The k-mers learned by GERV capture more sequence determinants of transcription factor binding than a motif-based approach alone, including both a transcription factor's canonical motif as well as associated co-factor motifs. We show that GERV outperforms existing methods in predicting SNPs associated with allele-specific binding. GERV correctly predicts a validated causal variant among linked SNPs, and prioritizes the variants previously reported to modulate the binding of FOXA1 in breast cancer cell lines. Thus, GERV provides a powerful...Continue Reading

Related Concepts

Alleles
Malignant Neoplasm of Breast
Deoxyribonucleases
Genome
Transcription Factor
Hepatocyte Nuclear Factor 3-alpha
Cell Line, Tumor
Evaluation
Approach
GPER protein, human

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