ArticleNature methods2010
cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity.PloS one · 2013Trial
- Dosage effect of copy number variation in epilepsy and ten regions of the human brain.Scientific reports · 2025Article
- Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland populations.Scientific reports · 2025Article
- Article
- Signatures of TSPAN8 variants associated with human metabolic regulation and diseases.iScience · 2021Article
- Detecting rare copy number variants from Illumina genotyping arrays with the CamCNV pipeline: Segmentation of z-scores improves detection and reliability.Genetic epidemiology · 2021Article
- Benefits and limitations of genome-wide association studies.Nature reviews. Genetics · 2019Review
- sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors.Nucleic acids research · 2017Article
- Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.PloS one · 2016Article
- The Role of Constitutional Copy Number Variants in Breast Cancer.Microarrays (Basel, Switzerland) · 2015Review
- Estimating copy numbers of alleles from population-scale high-throughput sequencing data.BMC bioinformatics · 2015Article
- Structural architecture of SNP effects on complex traits.American journal of human genetics · 2014Article
- Genetic variability in the regulation of gene expression in ten regions of the human brain.Nature neuroscience · 2014Article
- VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions.Frontiers in genetics · 2014Article
- A genome-wide association study and biological pathway analysis of epilepsy prognosis in a prospective cohort of newly treated epilepsy.Human molecular genetics · 2014Article
- HaplotypeCN: copy number haplotype inference with Hidden Markov Model and localized haplotype clustering.PloS one · 2014Article
- A method for calling copy number polymorphism using haplotypes.Frontiers in genetics · 2013Article
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.Frontiers in genetics · 2013Article
- cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.Genome biology · 2012Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Although genome-wide association studies have uncovered single-nucleotide polymorphisms (SNPs) associated with complex disease, these variants account for a small portion of heritability. Some contribution to this 'missing heritability' may come from copy-number variants (CNVs), in particular rare CNVs; but assessment of this contribution remains challenging because of the difficulty in accurately genotyping CNVs, particularly small variants. We report a population-based approach for the identification of CNVs that integrates data from multiple samples and platforms. Our algorithm, cnvHap, jointly learns a chromosome-wide haplotype model of CNVs and cluster-based models of allele intensity at each probe. Using data for 50 French individuals assayed on four separate platforms, we found that cnvHap correctly detected at least 14% more deleted and 50% more amplified genotypes than PennCNV or QuantiSNP, with an 82% and 115% improvement for aberrations containing <10 probes. Combining data from multiple platforms additionally improved sensitivity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.