Jun 13, 2014

On the identification of potential regulatory variants within genome wide association candidate SNP sets

BMC Medical Genomics
Chih-yu ChenWyeth W Wasserman

Abstract

Genome wide association studies (GWAS) are a population-scale approach to the identification of segments of the genome in which genetic variations may contribute to disease risk. Current methods focus on the discovery of single nucleotide polymorphisms (SNPs) associated with disease traits. As there are many SNPs within identified risk loci, and the majority of these are situated within non-coding regions, a key challenge is to identify and prioritize variants affecting regulatory sequences that are likely to contribute to the phenotype assessed. We focused investigation on SNPs within lung and breast cancer GWAS loci that reached genome-wide significance for potential roles in gene regulation with a specific focus on SNPs likely to disrupt transcription factor binding sites. Within risk loci, the regulatory potential of sub-regions was classified using relevant open chromatin and epigenetic high throughput sequencing data sets from the ENCODE project in available cancer and normal cell lines. Furthermore, transcription factor affinity altering variants were predicted by comparison of position weight matrix scores between disease and reference alleles. Lastly, ChIP-seq data of transcription associated factors and topological do...Continue Reading

  • References54
  • Citations20

References

  • References54
  • Citations20

Mentioned in this Paper

Genome-Wide Association Study
DNA, Junk
Normal Cell
Lung
Dysequilibrium Syndrome
Carcinoma of Lung
Chromatin Immunoprecipitation
Plasma Protein Binding Capacity
Position Frequency Matrices
Study of Epigenetics

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