Pathway-based analysis of GWAs data identifies association of sex determination genes with susceptibility to testicular germ cell tumors

Roelof Koster, Nandita Mitra, Kurt D'Andrea, Saran Vardhanabhuti, Charles C. Chung, Zhaoming Wang, R. Loren Erickson, David J. Vaughn, Kevin Litchfield, Nazneen Rahman, Mark H. Greene, Katherine A. McGlynn, Clare Turnbull, Stephen J. Chanock, Katherine L. Nathanson, Peter A. Kanetsky

Research output: Contribution to journalArticlepeer-review

Abstract

Genome-wide association (GWA) studies of testicular germ cell tumor (TGCT) have identified 18 susceptibility loci, some containing genes encoding proteins important in male germ cell development. Deletions of one of these genes, DMRT1, lead to male-to-female sex reversal and are associated with development of gonadoblastoma. To further explore genetic association with TGCT, we undertook a pathway-based analysis of SNP marker associations in the Penn GWAs (349 TGCT cases and 919 controls). We analyzed a custom-built sex determination gene set consisting of 32 genes using three different methods of pathway-based analysis. The sex determination gene set ranked highly compared with canonical gene sets, and it was associated with TGCT (FDRG = 2.28 × 10-5, FDRM = 0.014 and FDRI = 0.008 for Gene Set Analysis-SNP (GSA-SNP), Meta-Analysis Gene Set Enrichment of Variant Associations (MAGENTA) and Improved Gene Set Enrichment Analysis for Genomewide Association Study (i-GSEA4GWAS) analysis, respectively). The association remained after removal of DMRT1 from the gene set (FDRG = 0.0002, FDRM = 0.055 and FDRI = 0.009). Using data from the NCI GWA scan (582 TGCT cases and 1056 controls) and UK scan (986 TGCT cases and 4946 controls), we replicated these findings (NCI: FDRG = 0.006, FDRM = 0.014, FDRI = 0.033, and UK: FDRG = 1.04 × 10-6, FDRM = 0.016, FDRI = 0.025). After removal of DMRT1 from the gene set, the sex determination gene set remains associated with TGCT in the NCI (FDRG = 0.039, FDRM = 0.050 and FDRI = 0.055) and UK scans (FDRG = 3.00 × 10-5, FDRM = 0.056 and FDRI = 0.044). With the exception of DMRT1, genes in the sex determination gene set have not previously been identified as TGCT susceptibility loci in theseGWAscans, demonstrating the complementary nature of a pathway-based approach for genome-wide analysis of TGCT.

Original languageEnglish (US)
Pages (from-to)6061-6068
Number of pages8
JournalHuman molecular genetics
Volume23
Issue number22
DOIs
StatePublished - Nov 15 2014

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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