ArticlePLoS computational biology2010
Accurate distinction of pathogenic from benign CNVs in mental retardation.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 52 citations in OpenAlex.
- DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning.Bioinformatics (Oxford, England) · 2022Article
- Chromosomal variants accumulate in genomes of the spontaneous aborted fetuses revealed by chromosomal microarray analysis.PloS one · 2021Article
- Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements.Molecular syndromology · 2015Review
- Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data.PloS one · 2015Article
- Performance of case-control rare copy number variation annotation in classification of autism.BMC medical genomics · 2015Article
- SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay.BMC medical genomics · 2014Article
- Clinical interpretation of CNVs with cross-species phenotype data.Journal of medical genetics · 2014Article
- Deletions of chromosomal regulatory boundaries are associated with congenital disease.Genome biology · 2014Article
- Human molecular cytogenetics: From cells to nucleotides.Genetics and molecular biology · 2014Review
- Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease.Molecular cytogenetics · 2014Article
- In silico molecular cytogenetics: a bioinformatic approach to prioritization of candidate genes and copy number variations for basic and clinical genome research.Molecular cytogenetics · 2014Article
- PECONPI: a novel software for uncovering pathogenic copy number variations in non-syndromic sensorineural hearing loss and other genetically heterogeneous disorders.American journal of medical genetics. Part A · 2013Article
- Multiple samples aCGH analysis for rare CNVs detection.Journal of clinical bioinformatics · 2013Article
- Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish.Disease models & mechanisms · 2013Article
- Fusion of large-scale genomic knowledge and frequency data computationally prioritizes variants in epilepsy.PLoS genetics · 2013Article
- Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases.Current genomics · 2012Article
- Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders.American journal of human genetics · 2012Article
- Diagnostic interpretation of array data using public databases and internet sources.Human mutation · 2012Article
- Mouse genetic and phenotypic resources for human genetics.Human mutation · 2012Review
- Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience.Human mutation · 2012Article
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
Copy number variants (CNVs) have recently been recognized as a common form of genomic variation in humans. Hundreds of CNVs can be detected in any individual genome using genomic microarrays or whole genome sequencing technology, but their phenotypic consequences are still poorly understood. Rare CNVs have been reported as a frequent cause of neurological disorders such as mental retardation (MR), schizophrenia and autism, prompting widespread implementation of CNV screening in diagnostics. In previous studies we have shown that, in contrast to benign CNVs, MR-associated CNVs are significantly enriched in genes whose mouse orthologues, when disrupted, result in a nervous system phenotype. In this study we developed and validated a novel computational method for differentiating between benign and MR-associated CNVs using structural and functional genomic features to annotate each CNV. In total 13 genomic features were included in the final version of a Naïve Bayesian Tree classifier, with LINE density and mouse knock-out phenotypes contributing most to the classifier's accuracy. After demonstrating that our method (called GECCO) perfectly classifies CNVs causing known MR-associated syndromes, we show that it achieves high accuracy (94%) and negative predictive value (99%) on a blinded test set of more than 1,200 CNVs from a large cohort of individuals with MR. These results indicate that this classification method will be of value for objectively prioritizing CNVs in clinical research and diagnostics.
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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.