ArticleBioinformatics (Oxford, England)2016
Joint detection of copy number variations in parent-offspring trios.
Article in Bioinformatics (Oxford, England), 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.
- Article
- Dermokine mutations contribute to epithelial-mesenchymal transition and advanced melanoma through ERK/MAPK pathways.PloS one · 2023Article
- Screening for Copy Number Variations of the 15q13.3 Hotspot inCurrent issues in molecular biology · 2021Article
- Genome‑wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis.Oncology reports · 2020Article
- Detection of de novo copy number deletions from targeted sequencing of trios.Bioinformatics (Oxford, England) · 2019Article
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.Database : the journal of biological databases and curation · 2017Article
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Authors and funding
8 authors.
Funding
Abstract
motivationWhole genome sequencing (WGS) of parent-offspring trios is a powerful approach for identifying disease-associated genes via detecting copy number variations (CNVs). Existing approaches, which detect CNVs for each individual in a trio independently, usually yield low-detection accuracy. Joint modeling approaches leveraging Mendelian transmission within the parent-offspring trio can be an efficient strategy to improve CNV detection accuracy.
resultsIn this study, we developed TrioCNV, a novel approach for jointly detecting CNVs in parent-offspring trios from WGS data. Using negative binomial regression, we modeled the read depth signal while considering both GC content bias and mappability bias. Moreover, we incorporated the family relationship and used a hidden Markov model to jointly infer CNVs for three samples of a parent-offspring trio. Through application to both simulated data and a trio from 1000 Genomes Project, we showed that TrioCNV achieved superior performance than existing approaches. AVAILABILITY AND IMPLEMENTATION: The software TrioCNV implemented using a combination of Java and R is freely available from the website at https://github.com/yongzhuang/TrioCNV CONTACT: ydwang@hit.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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