ArticleGenome biology2019
Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.
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Who cites it
120 citing papers in PubMed.
- An Icelandic pangenome reference.Nature · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.Nucleic acids research · 2026Article
- Understanding the genetic imperfections of Lewy body dementia.Molecular neurodegeneration · 2026Review
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- A multi-ethnic reference map of T cell receptor germline diversity reveals evidence of natural selection on alpha chain genes.Nature communications · 2026Article
- The utility and advantages of exome and genome sequencing in pediatric kidney disease diagnosis.Childhood kidney diseases · 2026Review
- Systematic contextual biases in SegmentNT potentially relevant to other nucleotide transformer models.bioRxiv : the preprint server for biology · 2026Article
- Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.Bioinformatics (Oxford, England) · 2026Article
- Long-read sequencing of families reveals increased germline and postzygotic mutation rates in repetitive DNA.Nature communications · 2026Article
- Integrative analysis of in silico predictions and clinical evidence to delineate the capability of HiFi long-read sequencing in paralogous genes.NPJ genomic medicine · 2026Article
- Semi-automated genomic newborn screening highlights complexities in reporting.NPJ genomic medicine · 2026Article
- The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations.Cell genomics · 2026Article
- SDrecall: a sensitive approach for variant detection in segmental duplications.Genome biology · 2026Article
- Dark and camouflaged genomic regions remain challenging in CHM13.Scientific reports · 2026Article
- Nanopore sequencing and multiomics reveal predictable non-coding RNA activation in DNA methylation deficient Arabidopsis thaliana.Communications biology · 2025Article
- Locityper enables targeted genotyping of complex polymorphic genes.Nature genetics · 2025Article
- Long-read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
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- Article
60 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors.
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Abstract
backgroundThe human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads that we call dark by depth, and others that have ambiguous alignment, called camouflaged. We assess how well long-read or linked-read technologies resolve these regions.
resultsBased on standard whole-genome Illumina sequencing data, we identify 36,794 dark regions in 6054 gene bodies from pathways important to human health, development, and reproduction. Of these gene bodies, 8.7% are completely dark and 35.2% are ≥ 5% dark. We identify dark regions that are present in protein-coding exons across 748 genes. Linked-read or long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduce dark protein-coding regions to approximately 50.5%, 35.6%, and 9.6%, respectively. We present an algorithm to resolve most camouflaged regions and apply it to the Alzheimer's Disease Sequencing Project. We rescue a rare ten-nucleotide frameshift deletion in CR1, a top Alzheimer's disease gene, found in disease cases but not in controls.
conclusionsWhile we could not formally assess the association of the CR1 frameshift mutation with Alzheimer's disease due to insufficient sample-size, we believe it merits investigating in a larger cohort. There remain thousands of potentially important genomic regions overlooked by short-read sequencing that are largely resolved by long-read technologies.
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