Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism
| Autor: | Paul H. Noh, Yanping Wang, Debra J. Abrams, Rosetta M. Chiavacci, Alicia Olivant Fisher, Katia Sol-Church, Jennifer A. Hagerty, Deborah L. Stabley, Thomas F. Kolon, Kisha R. Harden, Ahmad H. BaniHani, T. Ernesto Figueroa, Julia Spencer Barthold, Hakon Hakonarson, Marcella Devoto, Ricardo Gonzalez, Jin Li, Cecilia E. Kim |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Male DNA Copy Number Variations Urology CNV European Continental Ancestry Group Single-nucleotide polymorphism 030105 genetics & heredity Genome White People Andrology Structural variation 03 medical and health sciences Gene duplication Cryptorchidism Genetics Medicine SNP Humans Copy-number variation Allele frequency Genotyping business.industry General Medicine 3. Good health 030104 developmental biology Reproductive Medicine Genome-Wide Association Study Software business Research Article |
| Zdroj: | BMC Urology |
| Popis: | Background Copy number variation (CNV) is a potential contributing factor to many genetic diseases. Here we investigated the potential association of CNV with nonsyndromic cryptorchidism, the most common male congenital genitourinary defect, in a Caucasian population. Methods Genome wide genotyping were performed in 559 cases and 1772 controls (Group 1) using Illumina HumanHap550 v1, HumanHap550 v3 or Human610-Quad platforms and in 353 cases and 1149 controls (Group 2) using the Illumina Human OmniExpress 12v1 or Human OmniExpress 12v1-1. Signal intensity data including log R ratio (LRR) and B allele frequency (BAF) for each single nucleotide polymorphism (SNP) were used for CNV detection using PennCNV software. After sample quality control, gene- and CNV-based association tests were performed using cleaned data from Group 1 (493 cases and 1586 controls) and Group 2 (307 cases and 1102 controls) using ParseCNV software. Meta-analysis was performed using gene-based test results as input to identify significant genes, and CNVs in or around significant genes were identified in CNV-based association test results. Called CNVs passing quality control and signal intensity visualization examination were considered for validation using TaqMan CNV assays and QuantStudio® 3D Digital PCR System. Results The meta-analysis identified 373 genome wide significant (p |
| Databáze: | OpenAIRE |
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