ArticleGenetics in medicine : official journal of the American College of Medical Genetics2018
Measuring coverage and accuracy of whole-exome sequencing in clinical context.
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 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
43 citing papers in PubMed, 83 citations in OpenAlex.
- Sensitivity of HiFi long-read genome sequencing for difficult-to-detect pathogenic variants when applied to real-world clinical laboratory samples.American journal of human genetics · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Exome sequencing identifies known and candidate genes in hearing impairment in Cameroon.Communications medicine · 2026Article
- Genetic insights: proband- only exome sequencing in pediatric neurological disorders.Journal of community genetics · 2026Article
- Article
- A Patient-Derived Organoid Platform from TUR-P Samples Enables Precision Drug Screening in Advanced Prostate Cancer.Cancers · 2025Article
- Genetic Landscape of Opsoclonus-Myoclonus-Ataxia Syndrome in Children.Pediatric neurology · 2025Article
- Advocating Targeted Sequential Screening over Whole Exome Sequencing in 21-Hydroxylase Deficiency.Indian journal of pediatrics · 2025Article
- Article
- Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases.HGG advances · 2025Article
- Precision Medicine in Hematologic Malignancies: Evolving Concepts and Clinical Applications.Biomedicines · 2025Review
- Radiation therapy results in preferential tumor antigen-specific lymphodepletion in head and neck cancer.Nature communications · 2025Article
- Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio.BMC genomics · 2025Article
- Paired comparison of the analytical performance between the Oncomine™ Comprehensive Assay v3 and whole-exome sequencing of ovarian cancer tissue.Molecular biology reports · 2024Article
- A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies.Malaria journal · 2024Article
- Improving somatic exome sequencing performance by biological replicates.BMC bioinformatics · 2024Article
- FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies.G3 (Bethesda, Md.) · 2023Article
- Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data.Nucleic acids research · 2023Article
- Whole-Exome and Transcriptome Sequencing Expands the Genotype of Majewski Osteodysplastic Primordial Dwarfism Type II.International journal of molecular sciences · 2023Article
- Identification of genotype-biochemical phenotype correlations associated with fructose 1,6-bisphosphatase deficiency.Communications biology · 2023Article
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 at 2 institutions in 1 country.
Funding
Abstract
purposeTo evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors.
methodsBlood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio.
resultsMean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability. For the two vendors with mean depth of coverage >120 ×, analytic positive predictive values (aPPVs) exceeded 99.1% for single-nucleotide variants and homozygous indels, and sensitivities were 98.9-99.9%; however, heterozygous indels showed lower accuracy and sensitivity. Among the trios, FNRs in the offspring were 0.07-0.62% at well-covered variants concordantly called in both parents.
conclusionThe current standard of 120 × coverage for clinical WES may be insufficient for consistent breadth of coverage across the exome. Ordering clinicians and researchers would benefit from vendors' reports that estimate sensitivity and aPPV, including depth of coverage across the exome.
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.