ArticleNature biotechnology2021
A pan-cancer landscape of somatic mutations in non-unique regions of the human genome.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 9 citations in OpenAlex.
- Nucleotide Substitution Biases in Related Cancer Driver Genes.International journal of molecular sciences · 2025Article
- Pan-Cancer Analysis and Experimental Validation of SOX4 as a Potential Diagnosis, Prognosis, and Immunotherapy Biomarker.Cancers · 2023Article
- Linked-read based analysis of the medulloblastoma genome.Frontiers in oncology · 2023Article
- Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma.The Journal of pathology · 2023Article
- DETexT: An SNV detection enhancement for low read depth by integrating mutational signatures into TextCNN.Frontiers in genetics · 2022Article
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
A substantial fraction of the human genome displays high sequence similarity with at least one other genomic sequence, posing a challenge for the identification of somatic mutations from short-read sequencing data. Here we annotate genomic variants in 2,658 cancers from the Pan-Cancer Analysis of Whole Genomes (PCAWG) cohort with links to similar sites across the human genome. We train a machine learning model to use signals distributed over multiple genomic sites to call somatic events in non-unique regions and validate the data against linked-read sequencing in an independent dataset. Using this approach, we uncover previously hidden mutations in ~1,700 coding sequences and in thousands of regulatory elements, including in known cancer genes, immunoglobulins and highly mutated gene families. Mutations in non-unique regions are consistent with mutations in unique regions in terms of mutation burden and substitution profiles. The analysis provides a systematic summary of the mutation events in non-unique regions at a genome-wide scale across multiple human cancers.
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Registered trials
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