ArticleNPJ genomic medicine2016
Clinical detection of deletion structural variants in whole-genome sequences.
Article in NPJ genomic medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- Molecular testing in holoprosencephaly.American journal of medical genetics. Part C, Seminars in medical genetics · 2018Pooled it
- Genetics and diagnostics of inherited retinal diseases in the era of whole genome sequencing.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2025Article
- Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review.NPJ genomic medicine · 2024Review
- JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level.Genomics, proteomics & bioinformatics · 2022Article
- A comprehensive benchmarking of WGS-based deletion structural variant callers.Briefings in bioinformatics · 2022Article
- ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data.Genome medicine · 2021Article
- Genetic Variation and the Distribution of Variant Types in the Horse.Frontiers in genetics · 2021Article
- Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer.Scientific reports · 2020Article
- Exon-focused targeted oligonucleotide microarray design increases detection of clinically relevant variants across multiple NHS genomic centres.NPJ genomic medicine · 2020Article
- From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.Genome medicine · 2019Article
- CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing.Scientific reports · 2019Article
- Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders.Journal of neurodevelopmental disorders · 2019Article
- Paediatric genomics: diagnosing rare disease in children.Nature reviews. Genetics · 2018Review
- A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data.American journal of human genetics · 2018Article
- Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases.NPJ genomic medicine · 2018Article
- The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants.NPJ genomic medicine · 2018Article
- Article
- Genome-wide characteristics ofNPJ genomic medicine · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 2 institutions in 1 country.
Funding
Abstract
Optimal management of acutely ill infants with monogenetic diseases requires rapid identification of causative haplotypes. Whole-genome sequencing (WGS) has been shown to identify pathogenic nucleotide variants in such infants. Deletion structural variants (DSVs, >50 nt) are implicated in many genetic diseases, and tools have been designed to identify DSVs using short-read WGS. Optimisation and integration of these tools into a WGS pipeline could improve diagnostic sensitivity and specificity of WGS. In addition, it may improve turnaround time when compared with current CNV assays, enhancing utility in acute settings. Here we describe DSV detection methods for use in WGS for rapid diagnosis in acutely ill infants: SKALD (Screening Konsensus and Annotation of Large Deletions) combines calls from two tools (Breakdancer and GenomeStrip) with calibrated filters and clinical interpretation rules. In four WGS runs, the average analytic precision (positive predictive value) of SKALD was 78%, and recall (sensitivity) was 27%, when compared with validated reference DSV calls. When retrospectively applied to a cohort of 36 families with acutely ill infants SKALD identified causative DSVs in two. The first was heterozygous deletion of exons 1-3 of
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.