ArticleGenome medicine2016
VARPRISM: incorporating variant prioritization in tests of de novo mutation association.
Article in Genome medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- De novo variants in HK1 associated with neurodevelopmental abnormalities and visual impairment.European journal of human genetics : EJHG · 2019Trial
- Evaluating the Genetic Overlap Between Congenital Heart Disease and Neuroblastoma Risk.Pediatric blood & cancer · 2026Article
- Statistical methods for assessing the effects of de novo variants on birth defects.Human genomics · 2024Review
- Genome interpretation using in silico predictors of variant impact.Human genetics · 2022Review
- Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability.G3 (Bethesda, Md.) · 2018Article
- XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundPatients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes.
resultsWe introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk. VARPRISM evaluates the consequence of any given exonic mutation on the protein sequence to estimate the likelihood that the mutation is benign or damaging and conducts a likelihood ratio test on the gene level. We analyzed the Simons Simplex Collection of 2508 parent-offspring autism trios using VARPRISM, replicating 44 genes previously implicated in autism susceptibility and identifying 20 additional candidate genes, including MYO1E, KCND3, PDCD1, DLX3, and TSPAN4 (false discovery rate < 0.3).
conclusionBy incorporating functional predictions, VARPRISM improved the statistical power to identify de novo mutations increasing disease risks. VARPRISM is available at http://www.hufflab.org/software/VARPRISM .
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Registered trials
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