Literature DB >> 25108383

Genome-wide association analyses identify variants in developmental genes associated with hypospadias.

Frank Geller1, Bjarke Feenstra1, Lisbeth Carstensen1, Tune H Pers2, Iris A L M van Rooij3, Izabella Baranowska Körberg4, Shweta Choudhry5, Juha M Karjalainen6, Tine H Schnack1, Mads V Hollegaard7, Wout F J Feitz8, Nel Roeleveld9, David M Hougaard7, Joel N Hirschhorn10, Lude Franke6, Laurence S Baskin5, Agneta Nordenskjöld4, Loes F M van der Zanden3, Mads Melbye11.   

Abstract

Hypospadias is a common congenital condition in boys in which the urethra opens on the underside of the penis. We performed a genome-wide association study on 1,006 surgery-confirmed hypospadias cases and 5,486 controls from Denmark. After replication genotyping of an 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). Together, these loci explain 9% of the liability to developing this condition. Several of the identified regions harbor genes with key roles in embryonic development (including HOXA4, IRX5, IRX6 and EYA1). Subsequent pathway analysis with GRAIL and DEPICT provided additional insight into possible genetic mechanisms causing hypospadias.

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Year:  2014        PMID: 25108383     DOI: 10.1038/ng.3063

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  55 in total

1.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Authors:  K J Livak; T D Schmittgen
Journal:  Methods       Date:  2001-12       Impact factor: 3.608

2.  Genomic control for association studies.

Authors:  B Devlin; K Roeder
Journal:  Biometrics       Date:  1999-12       Impact factor: 2.571

3.  Quantifying heterogeneity in a meta-analysis.

Authors:  Julian P T Higgins; Simon G Thompson
Journal:  Stat Med       Date:  2002-06-15       Impact factor: 2.373

4.  A linear complexity phasing method for thousands of genomes.

Authors:  Olivier Delaneau; Jonathan Marchini; Jean-François Zagury
Journal:  Nat Methods       Date:  2011-12-04       Impact factor: 28.547

Review 5.  Aetiology of hypospadias: a systematic review of genes and environment.

Authors:  L F M van der Zanden; I A L M van Rooij; W F J Feitz; B Franke; N V A M Knoers; N Roeleveld
Journal:  Hum Reprod Update       Date:  2012-02-26       Impact factor: 15.610

6.  Common variants in DGKK are strongly associated with risk of hypospadias.

Authors:  Loes F M van der Zanden; Iris A L M van Rooij; Wout F J Feitz; Jo Knight; A Rogier T Donders; Kirsten Y Renkema; Ernie M H F Bongers; Sita H H M Vermeulen; Lambertus A L M Kiemeney; Joris A Veltman; Alejandro Arias-Vásquez; Xufeng Zhang; Ellen Markljung; Liang Qiao; Laurence S Baskin; Agneta Nordenskjöld; Nel Roeleveld; Barbara Franke; Nine V A M Knoers
Journal:  Nat Genet       Date:  2010-11-28       Impact factor: 38.330

7.  Comparative gene expression analysis of genital tubercle development reveals a putative appendicular Wnt7 network for the epidermal differentiation.

Authors:  Han Sheng Chiu; John C Szucsik; Kylie M Georgas; Julia L Jones; Bree A Rumballe; Dave Tang; Sean M Grimmond; Alfor G Lewis; Bruce J Aronow; James L Lessard; Melissa H Little
Journal:  Dev Biol       Date:  2010-05-24       Impact factor: 3.582

8.  Reactome: a database of reactions, pathways and biological processes.

Authors:  David Croft; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; Shahana Mahajan; Bruce May; Nelson Ndegwa; Esther Schmidt; Veronica Shamovsky; Christina Yung; Ewan Birney; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

9.  Diacylglycerol kinase K variants impact hypospadias in a California study population.

Authors:  Suzan L Carmichael; Nebil Mohammed; Chen Ma; Dave Iovannisci; Shweta Choudhry; Larry S Baskin; John S Witte; Gary M Shaw; Edward J Lammer
Journal:  J Urol       Date:  2012-11-21       Impact factor: 7.450

10.  A travel guide to Cytoscape plugins.

Authors:  Rintaro Saito; Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Samad Lotia; Alexander R Pico; Gary D Bader; Trey Ideker
Journal:  Nat Methods       Date:  2012-11-06       Impact factor: 28.547

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  55 in total

1.  Battle of sex hormones in genitalia anomalies.

Authors:  Liang Ma
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-23       Impact factor: 11.205

2.  Single-nucleotide and copy-number variance related to severity of hypospadias.

Authors:  Neetu Singh; Devendra Kumar Gupta; Shilpa Sharma; Dinesh Kumar Sahu; Archana Mishra; Devendra Kumar Yadav; Jiledar Rawat; Arun Kumar Singh
Journal:  Pediatr Surg Int       Date:  2018-08-04       Impact factor: 1.827

Review 3.  Developments in our understanding of the genetic basis of birth defects.

Authors:  Daniel M Webber; Stewart L MacLeod; Michael J Bamshad; Gary M Shaw; Richard H Finnell; Sanjay S Shete; John S Witte; Stephen W Erickson; Linda D Murphy; Charlotte Hobbs
Journal:  Birth Defects Res A Clin Mol Teratol       Date:  2015-05-28

4.  Paediatric urology: GWAS identifies hypospadias loci.

Authors:  Annette Fenner
Journal:  Nat Rev Urol       Date:  2014-09-02       Impact factor: 14.432

5.  The role of genetic variation in DGKK on moderate and severe hypospadias.

Authors:  Melissa A Richard; Pagna Sok; Stephen Canon; Austin L Brown; Erin C Peckham-Gregory; Wendy N Nembhard; Suzan L Carmichael; Erik A Ehli; Noah A Kallsen; Shanna A Peyton; Gareth E Davies; Ashay Patel; Ismael Zamilpa; Richard A Wyatt; Charlotte A Hobbs; Michael E Scheurer; Philip J Lupo
Journal:  Birth Defects Res       Date:  2019-05-18       Impact factor: 2.344

6.  Tetraploid/Diploid Mosaicism in Cultured Genital Skin Fibroblasts: Is It Causally Related to Penoscrotal Hypospadias?

Authors:  Jacques C Giltay; Aart J Klijn; Tom P V M de Jong; Peter Kats; Marjolijn van Breugel; Susan Lens; Martijn Vromans; Lars T van der Veken; Ron Hochstenbach
Journal:  Mol Syndromol       Date:  2016-06-02

7.  Variation in the clinical and genetic evaluation of undervirilized boys with bifid scrotum and hypospadias.

Authors:  J M Swartz; R Ciarlo; E Denhoff; A Abrha; D A Diamond; J N Hirschhorn; Y-M Chan
Journal:  J Pediatr Urol       Date:  2017-01-30       Impact factor: 1.830

Review 8.  Current understanding of hypospadias: relevance of animal models.

Authors:  Gerald R Cunha; Adriane Sinclair; Gail Risbridger; John Hutson; Laurence S Baskin
Journal:  Nat Rev Urol       Date:  2015-04-07       Impact factor: 14.432

Review 9.  The Genetic and Environmental Factors Underlying Hypospadias.

Authors:  Aurore Bouty; Katie L Ayers; Andrew Pask; Yves Heloury; Andrew H Sinclair
Journal:  Sex Dev       Date:  2015-11-28       Impact factor: 1.824

10.  Timing of androgen receptor disruption and estrogen exposure underlies a spectrum of congenital penile anomalies.

Authors:  Zhengui Zheng; Brooke A Armfield; Martin J Cohn
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-23       Impact factor: 11.205

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