ArticleNucleic acids research2019
WisecondorX: improved copy number detection for routine shallow whole-genome sequencing.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 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
83 citing papers in PubMed.
- Genome sequencing for the diagnosis of intellectual disability as a paradigm for rare diseases in the French healthcare setting: the prospective DEFIDIAG study.Genome medicine · 2025Trial
- Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment.Nature communications · 2026Article
- Crucial parameters for precise copy number variation detection in formalin-fixed paraffin-embedded solid cancer samples.Molecular oncology · 2026Article
- Identification of autosomal and sex chromosome aneuploidies using next generation sequencing.Bioinformatics (Oxford, England) · 2026Article
- MARM: a framework for malignancy risk prediction from host-derived CNV in bronchoalveolar lavage fluid mNGS data with microbial admixture.Frontiers in microbiology · 2026Article
- Assessing the Detection Power of Genome-Wide Copy Number Variation Profiles in Prostate Cancer Using Simulated Shallow Whole-Genome Sequencing Data.JCO clinical cancer informatics · 2026Article
- Genomics and Epigenomics Approaches for the Quantification of Circulating Tumor DNA in Liquid Biopsy: Relevance of a Multimodal Strategy.International journal of molecular sciences · 2025Review
- ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing.Bioinformatics (Oxford, England) · 2025Article
- Detection of Human Brain Cancers using Genomic and Immune Cell Characterization of Cerebrospinal Fluid through CSF-BAM.Cancer discovery · 2025Article
- PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis.Briefings in bioinformatics · 2025Article
- Minimizing and quantifying uncertainty in AI-informed decisions: Applications in medicine.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Fragmentation signatures in cancer patients resemble those of patients with vascular or autoimmune diseases.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Insights Into the FOXE3 Transcriptional Network and Disease Mechanisms From the Investigation of a Regulatory Variant Driving Complex Microphthalmia.Investigative ophthalmology & visual science · 2025Article
- Genetic Subtype-Based International Prognostic Index Prognostic Model in Diffuse Large B-Cell Lymphoma.MedComm · 2025Article
- Comparative study of tools for copy number variation detection using next-generation sequencing data.Scientific reports · 2025Article
- Biphasic CAPA-IVM Improves Equine Oocyte Quality and Subsequent Embryo Development Without Inducing Genetic Aberrations.International journal of molecular sciences · 2025Article
- GCfix: a fast and accurate fragment length-specific method for correcting GC bias in cell-free DNA.Bioinformatics (Oxford, England) · 2025Article
- Whole-exome tumor-agnostic ctDNA analysis enhances minimal residual disease detection and reveals relapse mechanisms in localized colon cancer.Nature cancer · 2025Article
- Cracking rare disorders: a new minimally invasive RNA-seq protocol.NPJ genomic medicine · 2025Article
- KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data.BMC bioinformatics · 2025Article
23 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shallow whole-genome sequencing to infer copy number alterations (CNAs) in the human genome is rapidly becoming the method par excellence for routine diagnostic use. Numerous tools exist to deduce aberrations from massive parallel sequencing data, yet most are optimized for research and often fail to redeem paramount needs in a clinical setting. Optimally, a read depth-based analytical software should be able to deal with single-end and low-coverage data-this to make sequencing costs feasible. Other important factors include runtime, applicability to a variety of analyses and overall performance. We compared the most important aspect, being normalization, across six different CNA tools, selected for their assumed ability to satisfy the latter needs. In conclusion, WISECONDOR, which uses a within-sample normalization technique, undoubtedly produced the best results concerning variance, distributional assumptions and basic ability to detect true variations. Nonetheless, as is the case with every tool, WISECONDOR has limitations, which arise through its exclusiveness for non-invasive prenatal testing. Therefore, this work presents WisecondorX in addition, an improved WISECONDOR that enables its use for varying types of applications. WisecondorX is freely available at https://github.com/CenterForMedicalGeneticsGhent/WisecondorX.
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.