ArticleNucleic acids research2016
Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
64 citing papers in PubMed.
- Trial
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data.bioRxiv : the preprint server for biology · 2026Article
- Integrative genomic analysis identifies clinically relevant prognostic markers for colorectal cancer patients with liver metastasis.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- BayesCNV: A Bayesian Hierarchical Model for Sensitive and Specific Copy Number Estimation in Cell Free DNA.Diagnostics (Basel, Switzerland) · 2026Article
- Integrative genomic and immune landscape analysis of intimal sarcomas for emerging therapeutic targets and immunotherapy strategies.Frontiers in immunology · 2026Article
- Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models.European journal of human genetics : EJHG · 2025Article
- Biallelic variants of SEMA3F are associated with nonsyndromic hearing loss.Molecules and cells · 2025Article
- A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Unveiling Secondary Mutations in Blended Phenotypes: Dual ERCC4 and OTOA Pathogenic Variants Through WES Analysis.International journal of molecular sciences · 2024Article
- Whole-exome sequencing reveals the genetic causes and modifiers of moyamoya syndrome.Scientific reports · 2024Article
- RAS-ON inhibition overcomes clinical resistance to KRAS G12C-OFF covalent blockade.Nature communications · 2024Article
- Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis.Scientific reports · 2024Article
- Integrated genomic/epigenomic analysis stratifies subtypes of clear cell ovarian carcinoma, highlighting their cellular origin.Scientific reports · 2024Article
- Prenatal finding of isolated ventricular septal defect: genetic association, outcomes and counseling.Frontiers in genetics · 2024Review
- Case report: Duplication of theFrontiers in endocrinology · 2024Article
- Impaired neutrophil-mediated cell death drives Ewing's Sarcoma in the background of Down syndrome.Frontiers in oncology · 2024Article
- Discovery of a Novel Shared Variant AmongInternational journal of genomics · 2024Article
- Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus.Frontiers in genetics · 2024Review
- Exome sequencing in 116 patients with inherited thrombocytopenia that remained of unknown origin after systematic phenotype-driven diagnostic workup.Haematologica · 2023Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Copy Number Variants (CNVs) are structural rearrangements contributing to phenotypic variation that have been proved to be associated with many disease states. Over the last years, the identification of CNVs from whole-exome sequencing (WES) data has become a common practice for research and clinical purpose and, consequently, the demand for more and more efficient and accurate methods has increased. In this paper, we demonstrate that more than 30% of WES data map outside the targeted regions and that these reads, usually discarded, can be exploited to enhance the identification of CNVs from WES experiments. Here, we present EXCAVATOR2, the first read count based tool that exploits all the reads produced by WES experiments to detect CNVs with a genome-wide resolution. To evaluate the performance of our novel tool we use it for analysing two WES data sets, a population data set sequenced by the 1000 Genomes Project and a tumor data set made of bladder cancer samples. The results obtained from these analyses demonstrate that EXCAVATOR2 outperforms other four state-of-the-art methods and that our combined approach enlarge the spectrum of detectable CNVs from WES data with an unprecedented resolution. EXCAVATOR2 is freely available at http://sourceforge.net/projects/excavator2tool/.
Indexed as
Identifiers
What OpenQuestion holds
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.