DOI: 10.1101/514497Jan 9, 2019Paper

Systematic analysis of dark and camouflaged genes: disease-relevant genes hiding in plain sight

BioRxiv : the Preprint Server for Biology
Mark T W EbbertJohn D Fryer


Background: The 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 that are 'dark by depth' (few mappable reads) and others that are 'camouflaged' (ambiguous alignment), and we assess how well long-read technologies resolve these regions. We further present an algorithm to resolve most camouflaged regions (including in short-read data) and apply it to the Alzheimer's Disease Sequencing Project (ADSP; 13142 samples), as a proof of principle. Results: Based on standard whole-genome Illumina sequencing data, we identified 37873 dark regions in 5857 gene bodies (3635 protein-coding) from pathways important to human health, development, and reproduction. Of the 5857 gene bodies, 494 (8.4%) were 100% dark (142 protein-coding) and 2046 (34.9%) were ≥5% dark (628 protein-coding). Exactly 2757 dark regions were in protein-coding exons (CDS) across 744 genes. Long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduced dark CDS regions to approximately 45.1%, 33.3%, and 1...Continue Reading

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