GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation

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In the past 10 years, many genome wide association studies (GWAS) have been conducted to identify the genetic bases of complex human traits. As of January, 2014, more than 12,000 single-nucleotide polymorphisms (SNPs) have been reported to be significantly associated with at least one complex trait/disease. On one hand, about 85% of identified risk variants are located in non-coding regions, which motivates a systematic understanding of the function of non-coding variants in regulatory elements in the human genome. On the other hand, complex diseases are often affected by many genetic variants with small or moderate effects. To address these issues, we propose a statistical approach, GPA, to integrating information from multiple GWAS datasets and functional annotation. Notably, our approach only requires marker-wise p-values as input, making it especially useful when only summary statistics, instead of the full genotype and phenotype data, are available. We applied GPA to analyze GWAS datasets of five psychiatric disorders and bladder cancer, where the central nervous system genes, eQTLs from the Genotype-Tissue Expression (GTEx), and the ENCODE DNase-seq data from 125 cell lines were used as functional annotation. The analysis results suggest that GPA is an effective method for integrative data analysis in the post-GWAS era.

Vyšlo v časopise: GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation. PLoS Genet 10(11): e32767. doi:10.1371/journal.pgen.1004787
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004787

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