ArticleBMC genomics2012
Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity.PloS one · 2013Trial
- From genomic spectrum of NTRK genes to adverse effects of its inhibitors, a comprehensive genome-based and real-world pharmacovigilance analysis.Frontiers in pharmacology · 2024Article
- Genetic analysis of the equine orthologues for human CYP2D6: unraveling the complexity of the CYP2D family in horses.Frontiers in veterinary science · 2023Article
- Screening for Copy Number Variations of the 15q13.3 Hotspot inCurrent issues in molecular biology · 2021Article
- A comprehensive bioinformatic analysis of 126 patients with an inherited platelet disorder to identify both sequence and copy number genetic variants.Human mutation · 2020Article
- Clinical interpretation of copy number variants in the human genome.Journal of applied genetics · 2017Review
- Biological relevance of CNV calling methods using familial relatedness including monozygotic twins.BMC bioinformatics · 2014Article
- The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome.Genome research · 2013Article
- A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.BMC genomics · 2013Article
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.Frontiers in genetics · 2013Article
- Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus.Nature · 2011Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets.
resultsHere we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs.
conclusionOur new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.
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