Cell-of-origin chromatin organization shapes the mutational landscape of cancer.
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Abstract | Cancer is a disease potentiated by mutations in somatic cells. Cancer mutations are not distributed uniformly along the human genome. Instead, different human genomic regions vary by up to fivefold in the local density of cancer somatic mutations, posing a fundamental problem for statistical methods used in cancer genomics. Epigenomic organization has been proposed as a major determinant of the cancer mutational landscape. However, both somatic mutagenesis and epigenomic features are highly cell-type-specific. We investigated the distribution of mutations in multiple independent samples of diverse cancer types and compared them to cell-type-specific epigenomic features. Here we show that chromatin accessibility and modification, together with replication timing, explain up to 86% of the variance in mutation rates along cancer genomes. The best predictors of local somatic mutation density are epigenomic features derived from the most likely cell type of origin of the corresponding malignancy. Moreover, we find that cell-of-origin chromatin features are much stronger determinants of cancer mutation profiles than chromatin features of matched cancer cell lines. Furthermore, we show that the cell type of origin of a cancer can be accurately determined based on the distribution of mutations along its genome. Thus, the DNA sequence of a cancer genome encompasses a wealth of information about the identity and epigenomic features of its cell of origin. |
Year of Publication | 2015
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Journal | Nature
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Volume | 518
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Issue | 7539
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Pages | 360-4
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Date Published | 2015 Feb 19
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ISSN | 1476-4687
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URL | |
DOI | 10.1038/nature14221
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PubMed ID | 25693567
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PubMed Central ID | PMC4405175
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Grant list | P01 HL53750 / HL / NHLBI NIH HHS / United States
P01 HL053750 / HL / NHLBI NIH HHS / United States
U54 CA143874 / CA / NCI NIH HHS / United States
U01 ES017156 / ES / NIEHS NIH HHS / United States
U54 HG007010 / HG / NHGRI NIH HHS / United States
R01 MH101244 / MH / NIMH NIH HHS / United States
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