Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism.
BMC Urol
; 16(1): 62, 2016 Oct 21.
Article
in En
| MEDLINE
| ID: mdl-27769252
ABSTRACT
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 < 5X10-4) genes/loci including 49 genes/loci with deletions and 324 with duplications. Among them, 17 genes with deletion and 1 gene with duplication were identified in CNV-based association results in both Group 1 and Group 2. Only 2 genes (NUCB2 and UPF2) containing deletions passed CNV quality control in both groups and signal intensity visualization examination, but laboratory validation failed to verify these deletions.CONCLUSIONS:
Our data do not support that structural variation is a major cause of nonsyndromic cryptorchidism.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Cryptorchidism
/
White People
/
DNA Copy Number Variations
Type of study:
Prognostic_studies
/
Risk_factors_studies
Limits:
Humans
/
Male
Language:
En
Journal:
BMC Urol
Journal subject:
UROLOGIA
Year:
2016
Document type:
Article
Affiliation country:
Estados Unidos