Variants in developmental genes confer risk of hypospadias. F. Geller1, B. Feenstra1, L. Carstensen1, T. H. Pers2,3,4, I. A. L. M. van Rooij5, I. B. Körberg6, S. Choudhry7, J. Karjalainen8, T. H. Schnack1, M. V. Hollegaard9, W. F. J. Feitz10, N. Roeleveld5,11, D. M. Hougaard9, J. N. Hirschhorn2,3,12, L. S. Baskin7, A. Nordenskjöld6, L. F. M. van der Zanden5, M. Melbye1,13 1) Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark; 2) Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Childrens Hospital,Boston, USA; 3) Medical and Population Genetics Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, USA; 4) Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; 5) Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands; 6) Department of Women's and Children's Health and Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; 7) Department of Urology, University of California, San Francisco, USA; 8) Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands; 9) Danish Centre for Neonatal Screening, Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark; 10) Department of Urology, Pediatric Urology, Amalia Childrens Hospital, Radboud university medical center, Nijmegen, The Netherlands; 11) Department of Pediatrics, Amalia Childrens Hospital, Radboud university medical center, Nijmegen, The Netherlands; 12) Department of Genetics, Harvard Medical School, Boston, USA; 13) Department of Medicine, Stanford School of Medicine, Stanford, USA.
Hypospadias is a common congenital condition where the urethra opens on the underside of the penis. Family studies have indicated a strong genetic component in the etiology of hypospadias. We performed a genome-wide association study on 1,006 surgery-confirmed cases and 5,486 controls from Denmark. After replication genotyping of additional 1,972 cases and 1,812 controls from Denmark, the Netherlands and Sweden, 18 genomic regions showed independent association with P < 5×10-8; four more regions were associated with P < 1×10-6. Together these loci explain 9.4% of the liability to this malformation. Investigating the potential of the 548,642 genotyped SNPs resulted in an overall estimate of 56.9% of the variance explained. It was striking that several of the identified loci point to genes with roles in embryonic development, including four loci close to different members of the homeobox gene family (HOXA cluster, IRX5, IRX6, ZFHX3). Another strong candidate is EYA1, because it is known that deletion of Eya1 in mice is associated with multiple genitourinary tract defects including severe hypospadias. The associated loci near ADK and EEFSEC are connected to GWAS findings for tooth development and menarche, respectively, suggesting that these genes remain important after embryogenesis. Given these connections, we decided to perform comprehensive pathway analyses with GRAIL and DEPICT. The GRAIL analysis confirmed that multiple genes in different associated regions are functionally connected. We performed DEPICT analyses for all autosomal loci with P < 1×10-5 in the GWA scan. In a tissue cell type enrichment analysis, the three categories with the lowest P were particularly relevant for hypospadias: mesenchymal stem cells develop into stromal cells and fibroblasts are among the most common stromal cells, playing a key role in closing the urethral groove. Analyzing physiological systems gave significant results for the urogenital and the musculoskeletal system, warranting further study of genes with potential roles in both skeletal and urogenital development in embryos. Finally, a gene set analysis resulted in a large number of sets associated with development, morphology and abnormal growth showing significant enrichment. Overall, our study provides valuable insight into the genetic architecture of hypospadias by identifying many new risk loci and connecting nearby genes in developmental pathways that could also be important for other conditions.
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