title: Pathway analysis supports association of nonsyndromic cryptorchidism with genetic loci linked to cytoskeleton-dependent functions.
abstract: OBJECTIVE
  What are the genetic loci that increase susceptibility to nonsyndromic cryptorchidism, or undescended testis?
  
  
  CONCLUSIONS
  A genome-wide association study (GWAS) suggests that susceptibility to cryptorchidism is heterogeneous, with a subset of suggestive signals linked to cytoskeleton-dependent functions and syndromic forms of the disease.
  
  
  BACKGROUND
  Population studies suggest moderate genetic risk of cryptorchidism and possible maternal and environmental contributions to risk. Previous candidate gene analyses have failed to identify a major associated locus, although variants in insulin-like 3 (INSL3), relaxin/insulin-like family peptide receptor 2 (RXFP2) and other hormonal pathway genes may increase risk in a small percentage of patients.
  
  
  METHODS
  This is a case-control GWAS of 844 boys with nonsyndromic cryptorchidism and 2718 control subjects without syndromes or genital anomalies, all of European ancestry.
  
  
  METHODS
  All boys with cryptorchidism were diagnosed and treated by a pediatric specialist. In the discovery phase, DNA was extracted from tissue or blood samples and genotyping performed using the Illumina HumanHap550 and Human610-Quad (Group 1) or OmniExpress (Group 2) platform. We imputed genotypes genome-wide, and combined single marker association results in meta-analyses for all cases and for secondary subphenotype analyses based on testis position, laterality and age, and defined genome-wide significance as P = 7 × 10(-9) to correct for multiple testing. Selected markers were genotyped in an independent replication group of European cases (n = 298) and controls (n = 324). We used several bioinformatics tools to analyze top (P < 10(-5)) and suggestive (P < 10(-3)) signals for significant enrichment of signaling pathways, cellular functions and custom gene lists after multiple testing correction.
  
  
  RESULTS
  In the full analysis, we identified 20 top loci, none reaching genome-wide significance, but one passing this threshold in a subphenotype analysis of proximal testis position (rs55867206, near SH3PXD2B, odds ratio = 2.2 (95% confidence interval 1.7, 2.9), P = 2 × 10(-9)). An additional 127 top loci emerged in at least one secondary analysis, particularly of more severe phenotypes. Cytoskeleton-dependent molecular and cellular functions were prevalent in pathway analysis of suggestive signals, and may implicate loci encoding cytoskeletal proteins that participate in androgen receptor signaling. Genes linked to human syndromic cryptorchidism, including hypogonadotropic hypogonadism, and to hormone-responsive and/or differentially expressed genes in normal and cryptorchid rat gubernaculum, were also significantly overrepresented. No tested marker showed significant replication in an independent population. The results suggest heterogeneous, multilocus and potentially multifactorial susceptibility to nonsyndromic cryptorchidism.
  
  
  CONCLUSIONS
  The present study failed to identify genome-wide significant markers associated with cryptorchidism that could be replicated in an independent population, so further studies are required to define true positive signals among suggestive loci.
  
  
  CONCLUSIONS
  As the only GWAS to date of nonsyndromic cryptorchidism, these data will provide a basis for future efforts to understand genetic susceptibility to this common reproductive anomaly and the potential for additive risk from environmental exposures.
  
  
  BACKGROUND
  This work was supported by R01HD060769 (the Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD)), P20RR20173 (the National Center for Research Resources (NCRR), currently P20GM103464 from the National Institute of General Medical Sciences (NIGMS)), an Institute Development Fund to the Center for Applied Genomics at The Children's Hospital of Philadelphia, and Nemours Biomedical Research. The authors have no competing interests to declare.
authors.affiliation: Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA jbarthol@nemours.org.
authors.forename: Julia Spencer
authors.initials: JS
authors.lastname: Barthold
authors.affiliation: Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Division of Urology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Kolon
authors.affiliation: Department of Women's and Children's Health, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
authors.forename: Claude
authors.initials: C
authors.lastname: Kollin
authors.affiliation: Department of Women's and Children's Health, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
authors.forename: Agneta
authors.initials: A
authors.lastname: Nordenskjöld
authors.affiliation: Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA.
authors.forename: Alicia
authors.initials: A
authors.lastname: Olivant Fisher
authors.affiliation: Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA.
authors.forename: T Ernesto
authors.initials: TE
authors.lastname: Figueroa
authors.affiliation: Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA.
authors.forename: Ahmad H
authors.initials: AH
authors.lastname: BaniHani
authors.affiliation: Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Hagerty
authors.affiliation: Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA Present address: Auf der Bult Kinder- und Jugendkrankenhaus, Hannover, Germany.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Gonzaléz
authors.affiliation: Division of Urology, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA Present address: Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Paul H
authors.initials: PH
authors.lastname: Noh
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Rosetta M
authors.initials: RM
authors.lastname: Chiavacci
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Kisha R
authors.initials: KR
authors.lastname: Harden
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Debra J
authors.initials: DJ
authors.lastname: Abrams
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Cecilia E
authors.initials: CE
authors.lastname: Kim
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Hakon
authors.initials: H
authors.lastname: Hakonarson
authors.affiliation: Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Molecular Medicine, Sapienza University, Rome, Italy.
authors.forename: Marcella
authors.initials: M
authors.lastname: Devoto
mesh_terms: D016022:Case-Control Studies; D002648:Child; D002675:Child, Preschool; D003456:Cryptorchidism / Q000175:diagnosis* / Q000235:genetics; D003599:Cytoskeleton / Q000378:metabolism*; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D007328:Insulin / Q000235:genetics; D008297:Male; D016017:Odds Ratio; D010641:Phenotype; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics; D043562:Receptors, G-Protein-Coupled / Q000235:genetics; D015398:Signal Transduction; D013737:Testis / Q000473:pathology
chemical_list: D005819:Genetic Markers; D007328:Insulin; C084797:Leydig insulin-like protein; D011506:Proteins; C472867:RXFP2 protein, human; D043562:Receptors, G-Protein-Coupled
keywords: cryptorchidism; cytoskeleton; genetics; pathways; testis