ArticleNucleic acids research2024
Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- [Genetic diagnostics].Pathologie (Heidelberg, Germany) · 2026Review
- Comparison of Whole Exome Sequencing Commercial Kits Performance Across Diverse Tissue Sources.International journal of molecular sciences · 2026Article
- Precise exome analysis of blastocyst biopsy scale samples using primary template-directed amplification.BMC genomics · 2026Article
- ML-ExonCNV: a robust XGBoost multi-expert ensemble framework for rare exon CNV detection in whole-exome sequencing data.Briefings in bioinformatics · 2026Article
- Chronic Granulomatous Disease: Clinical and Molecular Characterization of Brazilian Patients.The journal of gene medicine · 2026Article
- ACE-Dependent Alzheimer's Disease: Blood ACE Phenotyping of the Most Prevalent and DamagingBiomedicines · 2026Article
- Toll-like receptors in innate immunity and inflammation: from fundamental biology to clinic insights.Immunity & inflammation · 2026Review
- Construction of a Genome-Wide Copy Number Variation Map and Association Analysis of Black Spot in Jujube.Plants (Basel, Switzerland) · 2025Article
- Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio.BMC genomics · 2025Article
- Importance of EQA/PT for the detection of genetic variants in comprehensive cancer genome testing.Scientific reports · 2025Article
- High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.Genome research · 2024Article
- Japanese Public Health Insurance System's new genomic strategic action to shorten the "diagnostic odyssey" for patients with rare and intractable diseases.Journal of human genetics · 2024Article
- Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.medRxiv : the preprint server for health sciences · 2024Article
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Authors and funding
27 authors.
Funding
Abstract
Next-generation DNA sequencing (NGS) in short-read mode has recently been used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, primarily focusing on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains unexplored at the single-nucleotide level despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions at the nucleotide-residue resolution using 10 genome sequence features based on real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). The newly acquired metric, designated the 'UNMET score,' along with additional lines of structural information from the human genome, allowed us to assess the sequencing challenges within the exonic region of interest using conventional short-read NGS. Thus, the UNMET score could provide a basis for addressing potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.
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