ArticleNature biotechnology2022
Curated variation benchmarks for challenging medically relevant autosomal genes.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers.
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163 citing papers in PubMed.
- Telomere-to-telomere CHM13 reference reveals missing truth variants and improves deep learning-based variant calling in long-read sequencing data.Quantitative biology (Beijing, China) · 2026Article
- Structural variant detection across sequencing technologies.Nature biotechnology · 2026Article
- An Icelandic pangenome reference.Nature · 2026Article
- Detecting pathogenic structural variation in families with undiagnosed rare disease in a national genome project.European journal of human genetics : EJHG · 2026Article
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Cost-efficient long-read trio-barcoded adaptive sequencing improves rare disease diagnosis.Nature communications · 2026Article
- High-grade serous ovarian cancer is associated with increased TP53 mutation burden in uterine lavage.NPJ precision oncology · 2026Article
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- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- Resolving a Complex Neonatal Phenotype by Rapid Trio Whole-Genome Sequencing: A De Novo 11q14.3-q22.3 Deletion and a Splicing-Altering Synonymous ANK1 Variant.Journal of clinical laboratory analysis · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- Pangenome-based human genome analysis improves trait association and genomic prediction.bioRxiv : the preprint server for biology · 2026Article
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- Complementarity of Long-Reads and Optical Mapping in Parkinson's Disease for Structural Variants.Annals of clinical and translational neurology · 2026Article
103 more citing papers are in PubMed but not listed here.
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37 authors.
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Abstract
The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome.
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