ArticleHuman mutation2017
panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.
Article in Human mutation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- The Tyrolean FounderBiomolecules · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Lynch Syndrome: An Update of Underlying Molecular Mechanisms, Phenotypes and Methods to Classify Variants of Uncertain Significance.Biomedicines · 2026Review
- Germline Genetic Testing in Breast and Gynecologic Cancers: Evaluating Age at Diagnosis as a Determinant.Cancers · 2026Article
- Generating a database by calculating the pathogenic variants and allele frequencies detected in hereditary cancers using genomic data: A nation study.Global medical genetics · 2025Article
- Congenital enteropathy caused by ezrin deficiency.Human genetics · 2025Article
- Efficient and easy gene expression and genetic variation data analysis and visualization using exvar.Scientific reports · 2025Article
- Understanding rare variant contributions to autism: lessons from dystrophin-deficient model.NPJ genomic medicine · 2025Article
- Exploring non-coding variants and evaluation of antisense oligonucleotides for splicing redirection in Usher syndrome.Molecular therapy. Nucleic acids · 2024Article
- Detection of germline CNVs from gene panel data: benchmarking the state of the art.Briefings in bioinformatics · 2024Article
- Article
- Parkinson's Disease Gene Screening in Familial Cases from Central and South America.Movement disorders : official journal of the Movement Disorder Society · 2024Article
- Next-Generation Sequencing-Based Copy Number Variation Analysis in Chinese Patients with Primary Ciliary Dyskinesia Revealed NovelPhenomics (Cham, Switzerland) · 2024Article
- Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.Briefings in bioinformatics · 2024Review
- Early Cancer Detection in Li-Fraumeni Syndrome with Cell-Free DNA.Cancer discovery · 2024Article
- BRACNAC: AInternational journal of molecular sciences · 2023Article
- Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle.Animals : an open access journal from MDPI · 2023Article
- Article
- Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases.Human genomics · 2023Article
- The Scarface Score: Deciphering Response to DNA Damage Agents in High-Grade Serous Ovarian Cancer-A GEICO Study.Cancers · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy-number variations (CNVs) in addition to single-nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics.
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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.