BMC Syst Biol 2012 17;6 Suppl 3:S13. Epub 2012 Dec 17.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
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BMC Syst Biol 2012 17;6 Suppl 3:S15. Epub 2012 Dec 17.
Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA.
Background: Interactions among genomic loci (also known as epistasis) have been suggested as one of the potential sources of missing heritability in single locus analysis of genome-wide association studies (GWAS). The computational burden of searching for interactions is compounded by the extremely low threshold for identifying significant p-values due to multiple hypothesis testing corrections. Utilizing prior biological knowledge to restrict the set of candidate SNP pairs to be tested can alleviate this problem, but systematic studies that investigate the relative merits of integrating different biological frameworks and GWAS data have not been conducted. Read More
Hum Reprod 2017 04;32(4):780-793
Endometriosis CaRe Centre, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.
Study Question: Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis?
Summary Answer: GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways.
What Is Known Already: Endometriosis is a complex disease with an estimated heritability of 50%. To date, GWAS revealed 10 genomic regions associated with endometriosis, explaining <4% of heritability, while half of the heritability is estimated to be due to common risk variants. Read More
BMC Genomics 2017 01 25;18(Suppl 1):1050. Epub 2017 Jan 25.
Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, Washington, 20037, D.C., USA.
Background: With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene set enrichment analysis have been frequently conducted. Integrative analysis can be conducted when multiple data sets are available. Read More
PLoS One 2011 23;6(11):e26527. Epub 2011 Nov 23.
Australian Prostate Cancer Research Centre-Queensland and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
Background: Kallikrein 15 (KLK15)/Prostinogen is a plausible candidate for prostate cancer susceptibility. Elevated KLK15 expression has been reported in prostate cancer and it has been described as an unfavorable prognostic marker for the disease.
Objectives: We performed a comprehensive analysis of association of variants in the KLK15 gene with prostate cancer risk and aggressiveness by genotyping tagSNPs, as well as putative functional SNPs identified by extensive bioinformatics analysis. Read More