ArticleBMC bioinformatics2017
SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing.BMC genomics · 2025Article
- Detection of copy number variations based on a local distance using next-generation sequencing data.Frontiers in genetics · 2023Article
- CNest: A novel copy number association discovery method uncovers 862 new associations from 200,629 whole-exome sequence datasets in the UK Biobank.Cell genomics · 2022Article
- Rapid Molecular Diagnosis of Genetically Inherited Neuromuscular Disorders Using Next-Generation Sequencing Technologies.Journal of clinical medicine · 2022Article
- A shortest path-based approach for copy number variation detection from next-generation sequencing data.Frontiers in genetics · 2022Article
- Ocular manifestations of Chinese patients with copy number variants in theMolecular vision · 2022Article
- Co-mutation pattern, clonal hierarchy, and clone size concur to determine disease phenotype of SRSF2Leukemia · 2021Article
- Whole-Gene Deletions ofGenes · 2021Article
- CNV-MEANN: A Neural Network and Mind Evolutionary Algorithm-Based Detection of Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- HBOS-CNV: A New Approach to Detect Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis.Molecular genetics & genomic medicine · 2020Article
- Clinical Applications of Chromosomal Microarray Testing in Myeloid Malignancies.Current hematologic malignancy reports · 2020Review
- A Density Peak-Based Method to Detect Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- Accurate Inference of Tumor Purity and Absolute Copy Numbers From High-Throughput Sequencing Data.Frontiers in genetics · 2020Article
- MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- Detection of fetal trisomy and single gene disease by massively parallel sequencing of extracellular vesicle DNA in maternal plasma: a proof-of-concept validation.BMC medical genomics · 2019Article
- High-throughput genotyping of a full voltage-gated sodium channel gene via genomic DNA using target capture sequencing and analytical pipeline MoNaS to discover novel insecticide resistance mutations.PLoS neglected tropical diseases · 2019Article
- Copy number variation analysis in 83 children with early-onset developmental and epileptic encephalopathy after targeted resequencing of a 109-epilepsy gene panel.Journal of human genetics · 2019Article
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12 authors.
Funding
Abstract
backgroundTargeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly to human genomic variability, some of which can lead to disease. However, effective detection of CNVs from targeted capture sequencing data remains challenging.
resultsHere we present SeqCNV, a novel CNV calling method designed to use capture NGS data. SeqCNV extracts the read depth information and utilizes the maximum penalized likelihood estimation (MPLE) model to identify the copy number ratio and CNV boundary. We applied SeqCNV to both bacterial artificial clone (BAC) and human patient NGS data to identify CNVs. These CNVs were validated by array comparative genomic hybridization (aCGH).
conclusionsSeqCNV is able to robustly identify CNVs of different size using capture NGS data. Compared with other CNV-calling methods, SeqCNV shows a significant improvement in both sensitivity and specificity.
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