The mutational landscape of human somatic and germline cells
Martincorena, I. & Campbell, P. J. Somatic mutation in cancer and normal cells. Science 349, 1483–1489 (2015).
Rouhani, F. J. et al. Mutational history of a human cell lineage from somatic to induced pluripotent stem cells. PLoS Genet. 12, e1005932 (2016).
Coorens, T. H. H. et al. Extensive phylogenies of human development reveal variable embryonic patterns. Preprint at bioRxiv https://doi.org/10.1101/2020.11.25.397828 (2020).
Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).
Bae, T. et al. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 359, 550–555 (2018).
Osorio, F. G. et al. Somatic mutations reveal lineage relationships and age-related mutagenesis in human hematopoiesis. Cell Rep. 25, 2308–2316.e4 (2018).
Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018).
Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).
Moore, L. et al. The mutational landscape of normal human endometrial epithelium. Nature 580, 640–646 (2020).
Zhu, M. et al. Somatic mutations increase hepatic clonal fitness and regeneration in chronic liver disease. Cell 177, 608–621.e12 (2019).
Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508–14513 (2012).
Abascal, F. et al. Somatic mutation landscapes at single-molecule resolution. Nature 593, 405–410 (2021).
Rahbari, R. et al. Timing, rates and spectra of human germline mutation. Nat. Genet. 48, 126–133 (2016).
Goldmann, J. M. et al. Parent-of-origin-specific signatures of de novo mutations. Nat. Genet. 48, 935–939 (2016).
Kong, A. et al. Rate of de novo mutations and the importance of father’s age to disease risk. Nature 488, 471–475 (2012).
Lynch, M. Rate, molecular spectrum, and consequences of human mutation. Proc. Natl Acad. Sci. USA 107, 961–968 (2010).
Milholland, B. et al. Differences between germline and somatic mutation rates in humans and mice. Nat. Commun. 8, 15183 (2017).
Visvader, J. E. & Clevers, H. Tissue-specific designs of stem cell hierarchies. Nat. Cell Biol. 18, 349–355 (2016).
Jónsson, H. et al. Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature 549, 519–522 (2017).
Ozturk, S. Telomerase activity and telomere length in male germ cells. Biol. Reprod. 92, 53 (2015).
Demanelis, K. et al. Determinants of telomere length across human tissues. Science 369, eaaz6876 (2020).
Fryxell, K. J. & Zuckerkandl, E. Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol. Biol. Evol. 17, 1371–1383 (2000).
Alexandrov, L. B. et al. Clock-like mutational processes in human somatic cells. Nat. Genet. 47, 1402–1407 (2015).
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
Boot, A. et al. In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. Genome Res. 28, 654–665 (2018).
Forbes, S. A. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 45, D777–D783 (2017).
Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 580, 269–273 (2020).
Li, X. C. et al. A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma. Ann. Oncol. 29, 938–944 (2018).
Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).
Alexandrov, L. B. et al. Mutational signatures associated with tobacco smoking in human cancer. Science 354, 618–622 (2016).
Di Persio, S. et al. Spermatogonial kinetics in humans. Development 144, 3430–3439 (2017).
Scally, A. Mutation rates and the evolution of germline structure. Phil. Trans. R. Soc. B 371, 20150137 (2016).
Frigola, J. et al. Reduced mutation rate in exons due to differential mismatch repair. Nat. Genet. 49, 1684–1692 (2017).
Rodriguez-Galindo, M., Casillas, S., Weghorn, D. & Barbadilla, A. Germline de novo mutation rates on exons versus introns in humans. Nat. Commun. 11, 3304 (2020).
GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318–1330 (2020).
Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).
Xia, B. et al. Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell 180, 248–262.e21 (2020).
Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033–1040 (2012).
Francioli, L. C. et al. Genome-wide patterns and properties of de novo mutations in humans. Nat. Genet. 47, 822–826 (2015).
Chen, C., Qi, H., Shen, Y., Pickrell, J. & Przeworski, M. Contrasting determinants of mutation rates in germline and soma. Genetics 207, 255–267 (2017).
.Walsh, C. et al. Somatic mutations in single human cardiomyocytes demonstrate accelerated age-related DNA damage and cell fusion. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-84503/v1 (2020).
Kirkwood, T. B. Evolution of ageing. Nature 270, 301–304 (1977).
Sakkas, D., Ramalingam, M., Garrido, N. & Barratt, C. L. R. Sperm selection in natural conception: what can we learn from Mother Nature to improve assisted reproduction outcomes? Hum. Reprod. Update 21, 711–726 (2015).
Brunner, S. F. et al. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 574, 538–542 (2019).
Lawson, A. R. J. et al. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 370, 75–82 (2020).
Olafsson, S. et al. Somatic evolution in non-neoplastic IBD-affected colon. Cell 182, 672–684.e11 (2020).
Ellis, P. et al. Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat. Protoc. 16, 841–871 (2021).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv https://arxiv.org/abs/1303.3997v2 (2013).
Tischler, G. & Leonard, S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol. Med. 9, 13 (2014).
Jones, D. et al. cgpCaVEManWrapper: simple execution of CaVEMan in order to detect somatic single nucleotide variants in NGS data. Curr. Protoc. Bioinformatics 56, 15.10.1–15.10.18 (2016).
Coorens, T. H. H. et al. Lineage-independent tumors in bilateral neuroblastoma. N. Engl. J. Med. 383, 1860–1865 (2020).
Yoshida, K. et al. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature 578, 266–272 (2020).
Raine, K. M. et al. cgpPindel: identifying somatically acquired insertion and deletion events from paired end sequencing. Curr. Protoc. Bioinformatics 52, 15.7.1–15.7.12 (2015).
Slater, G. S. C. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
Suzuki, M. et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 21, 1833–1840 (2011).
Coorens, T. H. H. et al. Embryonal precursors of Wilms tumor. Science 366, 1247–1251 (2019).
Blokzijl, F., Janssen, R., van Boxtel, R. & Cuppen, E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med. 10, 33 (2018).
Stamatoyannopoulos, J. A. et al. Human mutation rate associated with DNA replication timing. Nat. Genet. 41, 393–395 (2009).
Potten, C. S., Kellett, M., Rew, D. A. & Roberts, S. A. Proliferation in human gastrointestinal epithelium using bromodeoxyuridine in vivo: data for different sites, proximity to a tumour, and polyposis coli. Gut 33, 524–529 (1992).
Heller, C. G. & Clermont, Y. Spermatogenesis in man: an estimate of its duration. Science 140, 184–186 (1963).
Farmery, J. H. R., Smith, M. L., NIHR BioResource – Rare Diseases & Lynch, A. G. Telomerecat: a ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Sci. Rep. 8, 1300 (2018).
Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041.e21 (2017).