Clock-like mutational processes in human somatic cells

Alexandrov, Ludmil B.; Jones, Philip H.; Wedge, David C.; Sale, Julian E.; Campbell, Peter J.; Nik-Zainal, Serena; Stratton, Michael R.

doi:10.1038/ng.3441

Title: Clock-like mutational processes in human somatic cells

Journal Article · Mon Nov 09 00:00:00 EST 2015 · Nature Genetics

DOI:https://doi.org/10.1038/ng.3441· OSTI ID:1236704

^[1]; Jones, Philip H. ^[2]; Wedge, David C. ^[3]; Sale, Julian E. ^[4]; Campbell, Peter J. ^[2]; Nik-Zainal, Serena ^[5]; Stratton, Michael R. ^[3]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wellcome Trust Sanger Institute, Hinxton (United Kingdom)
Wellcome Trust Sanger Institute, Hinxton (United Kingdom); Univ. of Cambridge, Cambridge (United Kingdom)
Wellcome Trust Sanger Institute, Hinxton (United Kingdom)
MRC Lab. of Molecular Biology, Cambridge (United Kingdom)
Wellcome Trust Sanger Institute, Hinxton (United Kingdom); Addenbrooke's Hospital National Health Service (NHS) Trust, Cambridge (United Kingdom)

During the course of a lifetime, somatic cells acquire mutations. Different mutational processes may contribute to the mutations accumulated in a cell, with each imprinting a mutational signature on the cell's genome. Some processes generate mutations throughout life at a constant rate in all individuals, and the number of mutations in a cell attributable to these processes will be proportional to the chronological age of the person. Using mutations from 10,250 cancer genomes across 36 cancer types, we investigated clock-like mutational processes that have been operating in normal human cells. Two mutational signatures show clock-like properties. Both exhibit different mutation rates in different tissues. However, their mutation rates are not correlated, indicating that the underlying processes are subject to different biological influences. For one signature, the rate of cell division may influence its mutation rate. This paper provides the first survey of clock-like mutational processes operating in human somatic cells.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1236704

Report Number(s):: LA-UR-15-21254; ng.3441

Journal Information:: Nature Genetics, Vol. 47, Issue 12; ISSN 1061-4036

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 586 works

Citation information provided by
Web of Science

References (30)

The cancer genome Stratton, Michael R.; Campbell, Peter J.; Futreal, P. Andrew Nature, Vol. 458, Issue 7239 https://doi.org/10.1038/nature07943	journal	April 2009
Mutational signatures: the patterns of somatic mutations hidden in cancer genomes Alexandrov, Ludmil B.; Stratton, Michael R. Current Opinion in Genetics & Development, Vol. 24 https://doi.org/10.1016/j.gde.2013.11.014	journal	February 2014
Mechanisms underlying mutational signatures in human cancers Helleday, Thomas; Eshtad, Saeed; Nik-Zainal, Serena Nature Reviews Genetics, Vol. 15, Issue 9 https://doi.org/10.1038/nrg3729	journal	July 2014
Signatures of mutational processes in human cancer Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C. Nature, Vol. 500, Issue 7463 https://doi.org/10.1038/nature12477	journal	August 2013
Mutational Processes Molding the Genomes of 21 Breast Cancers Nik-Zainal, Serena; Alexandrov, Ludmil B.; Wedge, David C. Cell, Vol. 149, Issue 5 https://doi.org/10.1016/j.cell.2012.04.024	journal	May 2012
Deciphering Signatures of Mutational Processes Operative in Human Cancer Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C. Cell Reports, Vol. 3, Issue 1 https://doi.org/10.1016/j.celrep.2012.12.008	journal	January 2013
DNA Replication in Eukaryotic Cells Bell, Stephen P.; Dutta, Anindya Annual Review of Biochemistry, Vol. 71, Issue 1 https://doi.org/10.1146/annurev.biochem.71.110601.135425	journal	June 2002
DNA methylation age of human tissues and cell types Horvath, Steve Genome Biology, Vol. 14, Issue 10 https://doi.org/10.1186/gb-2013-14-10-r115	journal	January 2013
Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects Fousteri, Maria; Mullenders, Leon HF Cell Research, Vol. 18, Issue 1 https://doi.org/10.1038/cr.2008.6	journal	January 2008
The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma Davis, Caleb F.; Ricketts, Christopher J.; Wang, Min Cancer Cell, Vol. 26, Issue 3 https://doi.org/10.1016/j.ccr.2014.07.014	journal	September 2014
The Origin and Evolution of Mutations in Acute Myeloid Leukemia Welch, John S.; Ley, Timothy J.; Link, Daniel C. Cell, Vol. 150, Issue 2 https://doi.org/10.1016/j.cell.2012.06.023	journal	July 2012
Rate of de novo mutations and the importance of father’s age to disease risk Kong, Augustine; Frigge, Michael L.; Masson, Gisli Nature, Vol. 488, Issue 7412 https://doi.org/10.1038/nature11396	journal	August 2012
Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation Michaelson, Jacob J.; Shi, Yujian; Gujral, Madhusudan Cell, Vol. 151, Issue 7 https://doi.org/10.1016/j.cell.2012.11.019	journal	December 2012
Variation in genome-wide mutation rates within and between human families Nature Genetics, Vol. 43, Issue 7, p. 712-714 https://doi.org/10.1038/ng.862	journal	June 2011
Genome sequencing of normal cells reveals developmental lineages and mutational processes Behjati, Sam; Huch, Meritxell; van Boxtel, Ruben Nature, Vol. 513, Issue 7518 https://doi.org/10.1038/nature13448	journal	June 2014
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma Bolli, Niccolo; Avet-Loiseau, Hervé; Wedge, David C. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms3997	journal	January 2014
Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage Murchison, E. P.; Wedge, D. C.; Alexandrov, L. B. Science, Vol. 343, Issue 6169 https://doi.org/10.1126/science.1247167	journal	January 2014
Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer Nik-Zainal, Serena; Wedge, David C.; Alexandrov, Ludmil B. Nature Genetics, Vol. 46, Issue 5 https://doi.org/10.1038/ng.2955	journal	April 2014
Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing Gerlinger, Marco; Horswell, Stuart; Larkin, James Nature Genetics, Vol. 46, Issue 3 https://doi.org/10.1038/ng.2891	journal	February 2014
Subclonal diversification of primary breast cancer revealed by multiregion sequencing Yates, Lucy R.; Gerstung, Moritz; Knappskog, Stian Nature Medicine, Vol. 21, Issue 7 https://doi.org/10.1038/nm.3886	journal	June 2015
Analysis of mutational signatures in exomes from B-cell lymphoma cell lines suggest APOBEC3 family members to be involved in the pathogenesis of primary effusion lymphoma Wagener, R.; Alexandrov, L. B.; Montesinos-Rongen, M. Leukemia, Vol. 29, Issue 7 https://doi.org/10.1038/leu.2015.22	journal	February 2015
Robust regression using iteratively reweighted least-squares Holland, Paul W.; Welsch, Roy E. Communications in Statistics - Theory and Methods, Vol. 6, Issue 9 https://doi.org/10.1080/03610927708827533	journal	January 1977
Robust Statistics Huber, Peter J.; Ronchetti, Elvezio M. John Wiley & Sons, Inc https://doi.org/10.1002/9780470434697	book	January 2009
On a Robust Correlation Coefficient Abdullah, Mokhtar Bin The Statistician, Vol. 39, Issue 4 https://doi.org/10.2307/2349088	journal	January 1990
Disease-associated DNA methylation signatures in esophageal biopsies of children diagnosed with Eosinophilic Esophagitis Strisciuglio, Caterina; Payne, Felicity; Nayak, Komal Clinical Epigenetics, Vol. 13, Issue 1 https://doi.org/10.1186/s13148-021-01072-y	journal	April 2021
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Bolli, Niccolo; Avet-Loiseau, Hervé; Wedge, David C. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.33452	text	January 2014
Deciphering signatures of mutational processes operative in human cancer. Alexandrov, Ludmil B.; Nik-Zainal Abidin, Serena; Wedge, David C. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.60112	text	January 2013
Signatures of mutational processes in human cancer. Alexandrov, Ludmil B.; Nik-Zainal Abidin, Serena; Wedge, David C. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.31889	text	January 2013
Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nik-Zainal, Serena; Wedge, David C.; Alexandrov, Ludmil B. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.42271	text	January 2014
The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma E., Hacker, Kathryn; M., Leraas, Kristen; B., Smith, Angela The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/bd0j-6b91	text	January 2014

Cited By (205)

Transposable Elements Cross Kingdom Boundaries and Contribute to Inflammation and Ageing: Somatic Acquisition of Foreign Transposable Elements as a Catalyst of Genome Instability, Epigenetic Dysregulation, Inflammation, Senescence, and Ageing Chalmers, Timothy J.; Wu, Lindsay E. BioEssays, Vol. 42, Issue 3 https://doi.org/10.1002/bies.201900197	journal	March 2020
Cancer etiology: Variation in cancer risk among tissues is poorly explained by the number of gene mutations López-Lázaro, Miguel Genes, Chromosomes and Cancer, Vol. 57, Issue 6 https://doi.org/10.1002/gcc.22530	journal	February 2018
Most gene fusions in cancer are stochastic events Johansson, Bertil; Mertens, Fredrik; Schyman, Tommy Genes, Chromosomes and Cancer https://doi.org/10.1002/gcc.22745	journal	March 2019
Integrative genomic analysis identifies associations of molecular alterations to APOBEC and BRCA1/2 mutational signatures in breast cancer Trevino, Victor Molecular Genetics & Genomic Medicine, Vol. 7, Issue 8 https://doi.org/10.1002/mgg3.810	journal	June 2019
Mutational signature analysis identifies MUTYH deficiency in colorectal cancers and adrenocortical carcinomas: Mutational signature associated with MUTYH deficiency in cancers Pilati, Camilla; Shinde, Jayendra; Alexandrov, Ludmil B. The Journal of Pathology, Vol. 242, Issue 1 https://doi.org/10.1002/path.4880	journal	March 2017
Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma Negri, Gian Luca; Grande, Bruno M.; Delaidelli, Alberto The Journal of Pathology, Vol. 249, Issue 3 https://doi.org/10.1002/path.5319	journal	August 2019
Nucleotide Excision Repair: From Neurodegeneration to Cancer Liakos, Anastasios; Lavigne, Matthieu D.; Fousteri, Maria Advances in Experimental Medicine and Biology https://doi.org/10.1007/978-3-319-60733-7_2	book	January 2017
Genomics and clinical correlates of renal cell carcinoma Mitchell, Thomas J.; Rossi, Sabrina H.; Klatte, Tobias World Journal of Urology, Vol. 36, Issue 12 https://doi.org/10.1007/s00345-018-2429-x	journal	August 2018
Somatic mutations in neurons during aging and neurodegeneration Verheijen, Bert M.; Vermulst, Marc; van Leeuwen, Fred W. Acta Neuropathologica, Vol. 135, Issue 6 https://doi.org/10.1007/s00401-018-1850-y	journal	April 2018
The role of DNA damage as a therapeutic target in autosomal dominant polycystic kidney disease Zhang, Jennifer Q. J.; Saravanabavan, Sayanthooran; Munt, Alexandra Expert Reviews in Molecular Medicine, Vol. 21 https://doi.org/10.1017/erm.2019.6	journal	January 2019
The landscape of genomic alterations across childhood cancers Gröbner, Susanne N.; Worst, Barbara C.; Weischenfeldt, Joachim Nature, Vol. 555, Issue 7696 https://doi.org/10.1038/nature25480	journal	February 2018
Analysis of cancer genomes reveals basic features of human aging and its role in cancer development Podolskiy, Dmitriy I.; Lobanov, Alexei V.; Kryukov, Gregory V. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12157	journal	August 2016
Differences between germline and somatic mutation rates in humans and mice Milholland, Brandon; Dong, Xiao; Zhang, Lei Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15183	journal	May 2017
Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors Kim, Jaegil; Mouw, Kent W.; Polak, Paz Nature Genetics, Vol. 48, Issue 6 https://doi.org/10.1038/ng.3557	journal	April 2016
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas Campbell, Joshua D.; Alexandrov, Anton; Kim, Jaegil Nature Genetics, Vol. 48, Issue 6 https://doi.org/10.1038/ng.3564	journal	May 2016
An evolutionary perspective on field cancerization Curtius, Kit; Wright, Nicholas A.; Graham, Trevor A. Nature Reviews Cancer, Vol. 18, Issue 1 https://doi.org/10.1038/nrc.2017.102	journal	December 2017
Clonal evolution of colorectal cancer in IBD Choi, Chang-Ho R.; Bakir, Ibrahim Al; Hart, Ailsa L. Nature Reviews Gastroenterology & Hepatology, Vol. 14, Issue 4 https://doi.org/10.1038/nrgastro.2017.1	journal	February 2017
APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma Cannataro, Vincent L.; Gaffney, Stephen G.; Sasaki, Tomoaki Oncogene, Vol. 38, Issue 18 https://doi.org/10.1038/s41388-018-0657-6	journal	January 2019
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging Franco, Irene; Johansson, Anna; Olsson, Karl Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03244-6	journal	February 2018
The effects of mutational processes and selection on driver mutations across cancer types Temko, Daniel; Tomlinson, Ian P. M.; Severini, Simone Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04208-6	journal	May 2018
Genomic patterns of progression in smoldering multiple myeloma Bolli, Niccolò; Maura, Francesco; Minvielle, Stephane Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05058-y	journal	August 2018
Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma Wong, Kim; van der Weyden, Louise; Schott, Courtney R. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-018-08081-1	journal	January 2019
Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma Yan, Ting; Cui, Heyang; Zhou, Yong Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09255-1	journal	April 2019
ALPK1 hotspot mutation as a driver of human spiradenoma and spiradenocarcinoma Rashid, Mamunur; van der Horst, Michiel; Mentzel, Thomas Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09979-0	journal	May 2019
Brain somatic mutations observed in Alzheimer’s disease associated with aging and dysregulation of tau phosphorylation Park, Jun Sung; Lee, Junehawk; Jung, Eun Sun Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11000-7	journal	July 2019
Genomic landscape and chronological reconstruction of driver events in multiple myeloma Maura, Francesco; Bolli, Niccoló; Angelopoulos, Nicos Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11680-1	journal	August 2019
Integrated exome and RNA sequencing of dedifferentiated liposarcoma Hirata, Makoto; Asano, Naofumi; Katayama, Kotoe Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13286-z	journal	December 2019
Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer von Loga, Katharina; Woolston, Andrew; Punta, Marco Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-13915-7	journal	January 2020
The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly Pinese, Mark; Lacaze, Paul; Rath, Emma M. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-14079-0	journal	January 2020
Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations Nguyen, Bastien; Venet, David; Azim, Hatem A. npj Breast Cancer, Vol. 4, Issue 1 https://doi.org/10.1038/s41523-018-0077-3	journal	August 2018
Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours Avgustinova, Alexandra; Symeonidi, Aikaterini; Castellanos, Andrés Nature Cell Biology, Vol. 20, Issue 12 https://doi.org/10.1038/s41556-018-0233-x	journal	November 2018
Intra-tumour diversification in colorectal cancer at the single-cell level Roerink, Sophie F.; Sasaki, Nobuo; Lee-Six, Henry Nature, Vol. 556, Issue 7702 https://doi.org/10.1038/s41586-018-0024-3	journal	April 2018
The repertoire of mutational signatures in human cancer Alexandrov, Ludmil B.; Kim, Jaegil; Haradhvala, Nicholas J. Nature, Vol. 578, Issue 7793 https://doi.org/10.1038/s41586-020-1943-3	journal	February 2020
DNA methylation loss in late-replicating domains is linked to mitotic cell division Zhou, Wanding; Dinh, Huy Q.; Ramjan, Zachary Nature Genetics, Vol. 50, Issue 4 https://doi.org/10.1038/s41588-018-0073-4	journal	April 2018
Detecting the mutational signature of homologous recombination deficiency in clinical samples Gulhan, Doga C.; Lee, Jake June-Koo; Melloni, Giorgio E. M. Nature Genetics, Vol. 51, Issue 5 https://doi.org/10.1038/s41588-019-0390-2	journal	April 2019
The mutational footprints of cancer therapies Pich, Oriol; Muiños, Ferran; Lolkema, Martijn Paul Nature Genetics, Vol. 51, Issue 12 https://doi.org/10.1038/s41588-019-0525-5	journal	November 2019
Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma Noorani, Ayesha; Li, Xiaodun; Goddard, Martin Nature Genetics, Vol. 52, Issue 1 https://doi.org/10.1038/s41588-019-0551-3	journal	January 2020
Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions Teixeira, Vitor H.; Pipinikas, Christodoulos P.; Pennycuick, Adam Nature Medicine, Vol. 25, Issue 3 https://doi.org/10.1038/s41591-018-0323-0	journal	January 2019
Genomic features of renal cell carcinoma with venous tumor thrombus Warsow, Gregor; Hübschmann, Daniel; Kleinheinz, Kortine Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-25544-z	journal	May 2018
Burden of unique and low prevalence somatic mutations correlates with cancer survival Klebanov, Nikolai; Artomov, Mykyta; Goggins, William B. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41015-5	journal	March 2019
Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues Krimmel, Jeffrey D.; Schmitt, Michael W.; Harrell, Maria I. Proceedings of the National Academy of Sciences, Vol. 113, Issue 21 https://doi.org/10.1073/pnas.1601311113	journal	May 2016
Integrative genomic analysis of mouse and human hepatocellular carcinoma Dow, Michelle; Pyke, Rachel M.; Tsui, Brian Y. Proceedings of the National Academy of Sciences, Vol. 115, Issue 42 https://doi.org/10.1073/pnas.1811029115	journal	October 2018
Pancreatic cancer organoids recapitulate disease and allow personalized drug screening Driehuis, Else; van Hoeck, Arne; Moore, Kat Proceedings of the National Academy of Sciences, Vol. 116, Issue 52 https://doi.org/10.1073/pnas.1911273116	journal	December 2019
Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations Bronkhorst, Abel Jacobus; Ungerer, Vida; Holdenrieder, Stefan Critical Reviews in Clinical Laboratory Sciences https://doi.org/10.1080/10408363.2019.1700902	journal	December 2019
Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer Giessler, Klara M.; Kleinheinz, Kortine; Huebschmann, Daniel Journal of Experimental Medicine, Vol. 214, Issue 7 https://doi.org/10.1084/jem.20162017	journal	June 2017
Modeling clinical and molecular covariates of mutational process activity in cancer Robinson, Welles; Sharan, Roded; Leiserson, Mark D. M. Bioinformatics, Vol. 35, Issue 14 https://doi.org/10.1093/bioinformatics/btz340	journal	July 2019
Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26 Gudmundsson, Sanna; Wilbe, Maria; Ekvall, Sara Human Molecular Genetics, Vol. 26, Issue 6 https://doi.org/10.1093/hmg/ddx017	journal	February 2017
Neutral Theory and the Somatic Evolution of Cancer Cannataro, Vincent L.; Townsend, Jeffrey P. Molecular Biology and Evolution, Vol. 35, Issue 6 https://doi.org/10.1093/molbev/msy079	journal	April 2018
Mutations Beget More Mutations—Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation Ruan, Yongsen; Wang, Haiyu; Chen, Bingjie Molecular Biology and Evolution, Vol. 37, Issue 4 https://doi.org/10.1093/molbev/msz283	journal	December 2019
Uncovering a unique approach for damaged DNA replication: A computational investigation of a mutagenic tobacco-derived thymine lesion Wilson, Katie A.; Holland, Carl D.; Wetmore, Stacey D. Nucleic Acids Research, Vol. 47, Issue 4 https://doi.org/10.1093/nar/gky1265	journal	January 2019
Germline determinants of the somatic mutation landscape in 2,642 cancer genomes Waszak, Sebastian M.; Tiao, Grace; Zhu, Bin https://doi.org/10.1101/208330	posted_content	November 2017
Aging and neurodegeneration are associated with increased mutations in single human neurons Lodato, Michael A.; Rodin, Rachel E.; Bohrson, Craig L. Science https://doi.org/10.1101/221960	posted_content	November 2017
BAP1 Loss Predicts Therapeutic Vulnerability in Malignant Peritoneal Mesothelioma Shrestha, Raunak; Nabavi, Noushin; Lin, Yen-Yi Genome Medicine https://doi.org/10.1101/243477	posted_content	December 2018
De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures Ramazzotti, Daniele; Lal, Avantika; Liu, Keli https://doi.org/10.1101/384834	posted_content	June 2019
The Medical Genome Reference Bank: Whole genomes and phenotype of 2,570 healthy elderly Pinese, Mark; Lacaze, Paul; Rath, Emma M. https://doi.org/10.1101/473348	preprint	November 2018
Mutational analysis of field cancerization in bladder cancer Strandgaard, Trine; Nordentoft, Iver; Lamy, Philippe Bladder Cancer https://doi.org/10.1101/536466	posted_content	January 2019
Well-Differentiated Papillary Mesothelioma of the Peritoneum is Genetically Distinct from Malignant Mesothelioma Shrestha, Raunak; Nabavi, Noushin; Volik, Stanislav Cancers https://doi.org/10.1101/632810	posted_content	July 2019
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues Muyas, Francesc; Zapata, Luis; Guigó, Roderic Genome Medicine https://doi.org/10.1101/687822	posted_content	October 2019
An analysis of intrinsic base substitution patterns in diverse species reveals connections to cancer and metabolism Chan, Kin; Doherty, Kassidy N.; Alasmar, Salma Genetics https://doi.org/10.1101/758540	posted_content	March 2020
Mutation distribution density in tumors reconstructs human’s lost diversity Heredia-Genestar, José María; Marquès-Bonet, Tomàs; Juan, David Nature Communications https://doi.org/10.1101/773317	posted_content	September 2019
Matching cell lines with cancer type and subtype of origin via mutational, epigenomic and transcriptomic patterns Salvadores, Marina; Fuster-Tormo, Francisco; Supek, Fran https://doi.org/10.1101/809400	posted_content	October 2019
Sequencing Chemically Induced Mutations in the Mutamouse Lacz Reporter Gene Identifies Human Cancer Mutational Signatures Beal, Marc A.; Meier, Matt J.; LeBlanc, Danielle https://doi.org/10.1101/858159	posted_content	November 2019
APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication Seplyarskiy, Vladimir B.; Soldatov, Ruslan A.; Popadin, Konstantin Y. Genome Research, Vol. 26, Issue 2 https://doi.org/10.1101/gr.197046.115	journal	January 2016
One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin Abyzov, Alexej; Tomasini, Livia; Zhou, Bo Genome Research, Vol. 27, Issue 4 https://doi.org/10.1101/gr.215517.116	journal	February 2017
Molecular and clonal evolution in recurrent metastatic gliosarcoma Anderson, Kevin J.; Tan, Aaron C.; Parkinson, Jonathon Molecular Case Studies, Vol. 6, Issue 1 https://doi.org/10.1101/mcs.a004671	journal	January 2020
Incidence and prognostic significance of isolated trisomies in adult acute myeloid leukemia: A population-based study from the Swedish AML registry Lazarevic, Vladimir Lj; Rosso, Aldana; Juliusson, Gunnar European Journal of Haematology, Vol. 98, Issue 5 https://doi.org/10.1111/ejh.12861	journal	March 2017
Early divergence of mutational processes in human fetal tissues Kuijk, Ewart; Blokzijl, Francis; Jager, Myrthe Science Advances, Vol. 5, Issue 5 https://doi.org/10.1126/sciadv.aaw1271	journal	May 2019
DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification Chen, Lixin; Liu, Pingfang; Evans, Thomas C. Science, Vol. 355, Issue 6326 https://doi.org/10.1126/science.aai8690	journal	February 2017
Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors Anderson, Nathaniel D.; de Borja, Richard; Young, Matthew D. Science, Vol. 361, Issue 6405 https://doi.org/10.1126/science.aam8419	journal	August 2018
Somatic mutant clones colonize the human esophagus with age Martincorena, Iñigo; Fowler, Joanna C.; Wabik, Agnieszka Science, Vol. 362, Issue 6417 https://doi.org/10.1126/science.aau3879	journal	October 2018
Driver Mutations in Normal Airway Epithelium Elucidate Spatiotemporal Resolution of Lung Cancer Kadara, Humam; Sivakumar, Smruthy; Jakubek, Yasminka American Journal of Respiratory and Critical Care Medicine, Vol. 200, Issue 6 https://doi.org/10.1164/rccm.201806-1178oc	journal	September 2019
Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma Grande, Bruno M.; Gerhard, Daniela S.; Jiang, Aixiang Blood, Vol. 133, Issue 12 https://doi.org/10.1182/blood-2018-09-871418	journal	March 2019
Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples Díaz-Gay, Marcos; Vila-Casadesús, Maria; Franch-Expósito, Sebastià BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2234-y	journal	June 2018
Relation between DNA ionization potentials, single base substitutions and pathogenic variants Pucci, Fabrizio; Rooman, Marianne BMC Genomics, Vol. 20, Issue S8 https://doi.org/10.1186/s12864-019-5867-y	journal	July 2019
Genetic mutational analysis of pediatric acute lymphoblastic leukemia from a single center in China using exon sequencing Zhang, Honghong; Wang, Hongsheng; Qian, Xiaowen BMC Cancer, Vol. 20, Issue 1 https://doi.org/10.1186/s12885-020-6709-7	journal	March 2020
Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection Fiala, Clare; Diamandis, Eleftherios P. BMC Medicine, Vol. 16, Issue 1 https://doi.org/10.1186/s12916-018-1157-9	journal	October 2018
A comprehensive survey of the mutagenic impact of common cancer cytotoxics Szikriszt, Bernadett; Póti, Ádám; Pipek, Orsolya Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-0963-7	journal	May 2016
Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer Wojtowicz, Damian; Sason, Itay; Huang, Xiaoqing Genome Medicine, Vol. 11, Issue 1 https://doi.org/10.1186/s13073-019-0659-1	journal	July 2019
Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer Kim, Yoo-Ah; Wojtowicz, Damian; Sarto Basso, Rebecca Genome Medicine, Vol. 12, Issue 1 https://doi.org/10.1186/s13073-020-00745-2	journal	May 2020
A comparison of epigenetic mitotic-like clocks for cancer risk prediction Teschendorff, Andrew E. Genome Medicine, Vol. 12, Issue 1 https://doi.org/10.1186/s13073-020-00752-3	journal	June 2020
Interpreting the Dependence of Mutation Rates on Age and Time Gao, Ziyue; Wyman, Minyoung J.; Sella, Guy PLOS Biology, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pbio.1002355	journal	January 2016
Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine Goh, Gerald; Schmid, Ramona; Guiver, Kelly PLOS Medicine, Vol. 13, Issue 12 https://doi.org/10.1371/journal.pmed.1002136	journal	December 2016
Bioactivation mechanisms of N ‐hydroxyaristolactams: Nitroreduction metabolites of aristolochic acids Okuno, Yoshiharu; Bonala, Radha; Attaluri, Sivaprasad Environmental and Molecular Mutagenesis, Vol. 60, Issue 9 https://doi.org/10.1002/em.22321	journal	August 2019
Turning the tide in myelodysplastic/myeloproliferative neoplasms Deininger, Michael W. N.; Tyner, Jeffrey W.; Solary, Eric Nature Reviews Cancer, Vol. 17, Issue 7 https://doi.org/10.1038/nrc.2017.40	journal	June 2017
High-throughput sequencing of nodal marginal zone lymphomas identifies recurrent BRAF mutations Pillonel, V.; Juskevicius, D.; Ng, C. K. Y. Leukemia, Vol. 32, Issue 11 https://doi.org/10.1038/s41375-018-0082-4	journal	February 2018
Assessment of somatic single-nucleotide variation in brain tissue of cases with schizophrenia Fullard, John F.; Charney, Alexander W.; Voloudakis, Georgios Translational Psychiatry, Vol. 9, Issue 1 https://doi.org/10.1038/s41398-018-0342-0	journal	January 2019
Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing Nahar, Rahul; Zhai, Weiwei; Zhang, Tong Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02584-z	journal	January 2018
Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors George, Julie; Walter, Vonn; Peifer, Martin Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03099-x	journal	March 2018
The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature Inman, Gareth J.; Wang, Jun; Nagano, Ai Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06027-1	journal	September 2018
A practical guide for mutational signature analysis in hematological malignancies Maura, Francesco; Degasperi, Andrea; Nadeu, Ferran Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11037-8	journal	July 2019
Human glioblastoma arises from subventricular zone cells with low-level driver mutations Lee, Joo Ho; Lee, Jeong Eun; Kahng, Jee Ye Nature, Vol. 560, Issue 7717 https://doi.org/10.1038/s41586-018-0389-3	journal	August 2018
Tumour lineage shapes BRCA-mediated phenotypes Jonsson, Philip; Bandlamudi, Chaitanya; Cheng, Michael L. Nature, Vol. 571, Issue 7766 https://doi.org/10.1038/s41586-019-1382-1	journal	July 2019
Mutational processes shape the landscape of TP53 mutations in human cancer Giacomelli, Andrew O.; Yang, Xiaoping; Lintner, Robert E. Nature Genetics, Vol. 50, Issue 10 https://doi.org/10.1038/s41588-018-0204-y	journal	September 2018
A Simple 3-Parameter Model for Cancer Incidences Zhang, Xiaoxiao; Fröhlich, Holger; Grigoriev, Dima Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-21734-x	journal	February 2018
Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan Zhang, Lei; Dong, Xiao; Lee, Moonsook Proceedings of the National Academy of Sciences, Vol. 116, Issue 18 https://doi.org/10.1073/pnas.1902510116	journal	April 2019
Whole-genome sequencing of human malignant mesothelioma tumours and cell lines Oey, Harald; Daniels, Marissa; Relan, Vandana Carcinogenesis, Vol. 40, Issue 6 https://doi.org/10.1093/carcin/bgz066	journal	April 2019
Mutational signatures associated with tobacco smoking in human cancer Alexandrov, Ludmil B.; Ju, Young Seok; Haase, Kerstin bioRxiv https://doi.org/10.1101/051417	posted_content	May 2016
A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data Bertl, Johanna; Guo, Qianyun; Juul, Malene BMC Bioinformatics https://doi.org/10.1101/122879	posted_content	June 2017
Computational approaches for discovery of mutational signatures in cancer Baez-Ortega, Adrian; Gori, Kevin https://doi.org/10.1101/154716	posted_content	June 2017
In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors Boot, Arnoud; Huang, Mi Ni; Ng, Alvin W. T. Genome Research https://doi.org/10.1101/189233	posted_content	December 2017
Recapitulation of human germline coding variation in an ultra-mutated infant leukemia Gout, Alexander M.; Kotecha, Rishi S.; Kaur, Parwinder https://doi.org/10.1101/248690	preprint	May 2018
Reliable analysis of clinical tumor-only whole exome sequencing data Oh, Sehyun; Geistlinger, Ludwig; Ramos, Marcel JCO Clinical Cancer Informatics https://doi.org/10.1101/552711	posted_content	March 2019
Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer Kim, Yoo-Ah; Wojtowicz, Damian; Sarto, Rebecca Genome Medicine https://doi.org/10.1101/568568	posted_content	May 2019
Pediatric High Grade Glioma Resources From the Children’s Brain Tumor Tissue Consortium (CBTTC) and Pediatric Brain Tumor Atlas (PBTA) Ijaz, Heba; Koptyra, Mateusz; Gaonkar, Krutika S. Neuro-Oncology https://doi.org/10.1101/656587	posted_content	May 2019
Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making Chahal, Manik; Pleasance, Erin; Grewal, Jasleen Molecular Case Studies, Vol. 4, Issue 2 https://doi.org/10.1101/mcs.a002626	journal	April 2018
Whole genome sequencing analysis for cancer genomics and precision medicine Nakagawa, Hidewaki; Fujita, Masashi Cancer Science, Vol. 109, Issue 3 https://doi.org/10.1111/cas.13505	journal	February 2018
The evolutionary history of dogs in the Americas Ní Leathlobhair, Máire; Perri, Angela R.; Irving-Pease, Evan K. Science, Vol. 361, Issue 6397 https://doi.org/10.1126/science.aao4776	journal	July 2018
RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues Yizhak, Keren; Aguet, François; Kim, Jaegil Science, Vol. 364, Issue 6444 https://doi.org/10.1126/science.aaw0726	journal	June 2019
APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa Cho, Raymond J.; Alexandrov, Ludmil B.; den Breems, Nicoline Y. Science Translational Medicine, Vol. 10, Issue 455 https://doi.org/10.1126/scitranslmed.aas9668	journal	August 2018
SigsPack, a package for cancer mutational signatures Schumann, Franziska; Blanc, Eric; Messerschmidt, Clemens BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3043-7	journal	September 2019
Portrait of a cancer: mutational signature analyses for cancer diagnostics Van Hoeck, Arne; Tjoonk, Niels H.; van Boxtel, Ruben BMC Cancer, Vol. 19, Issue 1 https://doi.org/10.1186/s12885-019-5677-2	journal	May 2019
Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development Chen, Yuting; Widschwendter, Martin; Teschendorff, Andrew E. Genome Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s13059-017-1366-0	journal	December 2017
Timing somatic events in the evolution of cancer Jolly, Clemency; Van Loo, Peter Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1476-3	journal	July 2018
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues Muyas, Francesc; Zapata, Luis; Guigó, Roderic Genome Medicine, Vol. 12, Issue 1 https://doi.org/10.1186/s13073-020-00746-1	journal	May 2020
Medulloblastoma therapy generates risk of a poorly-prognostic H3 wild-type subgroup of diffuse intrinsic pontine glioma: a report from the International DIPG Registry Gits, Hunter C.; Anderson, Maia; Stallard, Stefanie Acta Neuropathologica Communications, Vol. 6, Issue 1 https://doi.org/10.1186/s40478-018-0570-9	journal	July 2018
Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models Funnell, Tyler; Zhang, Allen W.; Grewal, Diljot PLOS Computational Biology, Vol. 15, Issue 2 https://doi.org/10.1371/journal.pcbi.1006799	journal	February 2019
Somatic mutant clones colonize the human esophagus with age. Martincorena, Iñigo; Fowler, Joanna C.; Wabik, Agnieszka Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.31457	text	January 2018
Genomics and clinical correlates of renal cell carcinoma. Mitchell, Thomas; Rossi, Sabrina; Klatte, Tobias Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.32266	text	January 2018
The evolutionary history of 2,658 cancers. Gerstung, Moritz; Jolly, Clemency; Leshchiner, Ignaty Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.50319	text	January 2020
Cancer Etiology: Variation in Cancer Risk among Tissues is Poorly Explained by the Number of Gene Mutations Lopez-Lazaro, Miguel https://doi.org/10.20944/preprints201708.0103.v1	preprint	August 2017
Epigenetic drift, epigenetic clocks and cancer risk Zheng, Shijie C.; Widschwendter, Martin; Teschendorff, Andrew E. Epigenomics, Vol. 8, Issue 5 https://doi.org/10.2217/epi-2015-0017	journal	May 2016
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Rubanova, Yulia; Shi, Ruian; Harrigan, Caitlin F. The Francis Crick Institute https://doi.org/10.25418/crick.11876955.v1	text	January 2020
Single-cell analysis based dissection of clonality in myelofibrosis Mylonas, Elena; Yoshida, Kenichi; Frick, Mareike Nature Publishing Group https://doi.org/10.5167/uzh-187721	text	January 2020
Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery Simonetti, Giorgia; Padella, Antonella; do Valle, Italo Farìa Cancer, Vol. 125, Issue 5 https://doi.org/10.1002/cncr.31837	journal	November 2018
Somatic mutation load and spectra: A record of DNA damage and repair in healthy human cells: Human Somatic Mutation Load and Spectra Saini, Natalie; Gordenin, Dmitry A. Environmental and Molecular Mutagenesis, Vol. 59, Issue 8 https://doi.org/10.1002/em.22215	journal	August 2018
Mechanisms shaping the mutational landscape of the FRA3B/ FHIT -deficient cancer genome Saldivar, Joshua C.; Park, Dongju Genes, Chromosomes and Cancer, Vol. 58, Issue 5 https://doi.org/10.1002/gcc.22684	journal	November 2018
Somatic genome alterations in relation to age in lung adenocarcinoma Meucci, Stefano; Keilholz, Ulrich; Heim, Daniel International Journal of Cancer, Vol. 145, Issue 8 https://doi.org/10.1002/ijc.32265	journal	March 2019
Nonnegative tensor decomposition with custom clustering for microphase separation of block copolymers Alexandrov, Boian S.; Stanev, Valentin G.; Vesselinov, Velimir V. Statistical Analysis and Data Mining: The ASA Data Science Journal, Vol. 12, Issue 4 https://doi.org/10.1002/sam.11407	journal	February 2019
Tissue-specific mutation accumulation in human adult stem cells during life Blokzijl, Francis; de Ligt, Joep; Jager, Myrthe Nature, Vol. 538, Issue 7624 https://doi.org/10.1038/nature19768	journal	October 2016
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours Ma, Xiaotu; Liu, Yu; Liu, Yanling Nature, Vol. 555, Issue 7696 https://doi.org/10.1038/nature25795	journal	February 2018
Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis Letouzé, Eric; Shinde, Jayendra; Renault, Victor Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01358-x	journal	November 2017
Integrated analysis of the immunological and genetic status in and across cancer types: impact of mutational signatures beyond tumor mutational burden Budczies, Jan; Seidel, Anja; Christopoulos, Petros OncoImmunology, Vol. 7, Issue 12 https://doi.org/10.1080/2162402x.2018.1526613	journal	September 2018
Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference Matsutani, Taro; Ueno, Yuki; Fukunaga, Tsukasa Bioinformatics, Vol. 35, Issue 22 https://doi.org/10.1093/bioinformatics/btz266	journal	April 2019
Understanding mutagenesis through delineation of mutational signatures in human cancer Petljak, Mia; Alexandrov, Ludmil B. Carcinogenesis, Vol. 37, Issue 6 https://doi.org/10.1093/carcin/bgw055	journal	May 2016
A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data Bertl, Johanna; Guo, Qianyun; Juul, Malene BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2141-2	journal	April 2018
The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population Youk, Jeonghwan; An, Yohan; Park, Seongyeol BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6674-1	journal	March 2020
Different mutational characteristics of the subsets of EGFR-tyrosine kinase inhibitor sensitizing mutation-positive lung adenocarcinoma Kim, Eun Young; Kim, Arum; Lee, Gaeun BMC Cancer, Vol. 18, Issue 1 https://doi.org/10.1186/s12885-018-5116-9	journal	December 2018
New insights into the generation and role of de novo mutations in health and disease Acuna-Hidalgo, Rocio; Veltman, Joris A.; Hoischen, Alexander Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1110-1	journal	November 2016
Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations Anandakrishnan, Ramu; Varghese, Robin T.; Kinney, Nicholas A. PLOS Computational Biology, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pcbi.1006881	journal	March 2019
Aging and the rise of somatic cancer-associated mutations in normal tissues Risques, Rosa Ana; Kennedy, Scott R. PLOS Genetics, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pgen.1007108	journal	January 2018
Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Wong, Kim; Van Der Weyden, Louise; Schott, Courtney R. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.37190	text	January 2019
The repertoire of mutational signatures in human cancer Alexandrov, Ludmil B.; Kim, Jaegil; Haradhvala, Nicholas J. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.64271	text	January 2020
Computational Methods for Characterizing Cancer Mutational Heterogeneity Vandin, Fabio Frontiers in Genetics, Vol. 8 https://doi.org/10.3389/fgene.2017.00083	journal	June 2017
Genomic Alteration Burden in Advanced Prostate Cancer and Therapeutic Implications Ryan, Matthew J.; Bose, Rohit Frontiers in Oncology, Vol. 9 https://doi.org/10.3389/fonc.2019.01287	journal	November 2019
Interpreting the Dependence of Mutation Rates on Age and Time Gao, Ziyue; Wyman, Minyoung J.; Sella, Guy Columbia University https://doi.org/10.7916/d8v69jg5	text	January 2016
Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer Ishaque, Naveed; Abba, Mohammed L.; Hauser, Christine Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07041-z	journal	November 2018
Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations Seplyarskiy, Vladimir B.; Akkuratov, Evgeny E.; Akkuratova, Natalia Nature Genetics, Vol. 51, Issue 1 https://doi.org/10.1038/s41588-018-0285-7	journal	December 2018
The MiAge Calculator: a DNA methylation-based mitotic age calculator of human tissue types Youn, Ahrim; Wang, Shuang Epigenetics, Vol. 13, Issue 2 https://doi.org/10.1080/15592294.2017.1389361	journal	February 2018
Somatic Mutations and Genome Stability Maintenance in Clonal Coral Colonies López, Elora H.; Palumbi, Stephen R. Molecular Biology and Evolution, Vol. 37, Issue 3 https://doi.org/10.1093/molbev/msz270	journal	November 2019
Mutations beget more mutations – The baseline mutation rate and runaway accumulation Ruan, Yongsen; Chen, Bingjie; Chen, Qingjian Molecular Biology and Evolution https://doi.org/10.1101/690099	posted_content	July 2019
In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors Boot, Arnoud; Huang, Mi Ni; Ng, Alvin W. T. Genome Research, Vol. 28, Issue 5 https://doi.org/10.1101/gr.230219.117	journal	April 2018
Mutational landscape in genetically engineered, carcinogen-induced, and radiation-induced mouse sarcoma Lee, Chang-Lung; Mowery, Yvonne M.; Daniel, Andrea R. JCI Insight, Vol. 4, Issue 13 https://doi.org/10.1172/jci.insight.128698	journal	July 2019
Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia Li, Benshang; Brady, Samuel W.; Ma, Xiaotu Blood, Vol. 135, Issue 1 https://doi.org/10.1182/blood.2019002220	journal	January 2020
A pilot study of pembrolizumab in smoldering myeloma: report of the clinical, immune, and genomic analysis Manasanch, Elisabet E.; Han, Guangchun; Mathur, Rohit Blood Advances, Vol. 3, Issue 15 https://doi.org/10.1182/bloodadvances.2019000300	journal	August 2019
Correlation of an epigenetic mitotic clock with cancer risk. Yang, Zhen; Wong, Andrew; Kuh, Diana Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.21456	text	January 2016
A practical guide for mutational signature analysis in hematological malignancies. Maura, Francesco; Degasperi, Andrea; Nadeu, Ferran Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.41719	text	January 2019
Comprehensive molecular characterization of mitochondrial genomes in human cancers Yuan, Yuan; Ju, Young Seok; Kim, Youngwook Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.64262	text	January 2020
Mutational Analysis of Field Cancerization in Bladder Cancer Strandgaard, Trine; Nordentoft, Iver; Lamy, Philippe Bladder Cancer, Vol. 6, Issue 3 https://doi.org/10.3233/blc-200282	journal	September 2020
Significance of Wild-Type p53 Signaling in Suppressing Apoptosis in Response to Chemical Genotoxic Agents: Impact on Chemotherapy Outcome Mirzayans, Razmik; Andrais, Bonnie; Kumar, Piyush International Journal of Molecular Sciences, Vol. 18, Issue 5 https://doi.org/10.3390/ijms18050928	journal	April 2017
Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity Rošić, Silvana; Amouroux, Rachel; Requena, Cristina E. Nature Genetics, Vol. 50, Issue 3 https://doi.org/10.1038/s41588-018-0061-8	journal	February 2018
The effects of mutational processes and selection on driver mutations across cancer types Temko, Daniel; Tomlinson, Ian P. M.; Severini, Simone bioRxiv https://doi.org/10.1101/149096	posted_content	June 2017
Somatic mutations and genome stability maintenance in clonal coral colonies López, Elora H.; Palumbi, Stephen R. bioRxiv https://doi.org/10.1101/799643	posted_content	October 2019
Aging and neurodegeneration are associated with increased mutations in single human neurons Lodato, Michael A.; Rodin, Rachel E.; Bohrson, Craig L. Science, Vol. 359, Issue 6375 https://doi.org/10.1126/science.aao4426	journal	December 2017
De novo mutational signature discovery in tumor genomes using SparseSignatures Lal, Avantika; Liu, Keli; Tibshirani, Robert PLOS Computational Biology, Vol. 17, Issue 6 https://doi.org/10.1371/journal.pcbi.1009119	journal	June 2021
Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma. Noorani, Ayesha; Li, Xiaodun; Goddard, Martin Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.46582	text	January 2020
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Davies, Helen; Glodzik, Dominik; Morganella, Sandro Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.61944	text	January 2017
The evolutionary history of 2,658 cancers. Gerstung, Moritz; Jolly, Clemency; Leshchiner, Ignaty The Francis Crick Institute https://doi.org/10.25418/crick.11842797.v1	text	January 2020
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Rubanova, Yulia; Shi, Ruian; Harrigan, Caitlin F. The Francis Crick Institute https://doi.org/10.25418/crick.11876955	text	January 2020
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures Davies, Helen; Glodzik, Dominik; Morganella, Sandro Nature Medicine, Vol. 23, Issue 4 https://doi.org/10.1038/nm.4292	journal	March 2017
The mutational footprints of cancer therapies Pich, Oriol; Muiños, Ferran; Lolkema, Martijn Paul https://doi.org/10.1101/683268	posted_content	June 2019
Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin Cleal, Kez; Jones, Rhiannon E.; Grimstead, Julia W. Genome Research, Vol. 29, Issue 5 https://doi.org/10.1101/gr.240705.118	journal	March 2019
Correlation of an epigenetic mitotic clock with cancer risk Yang, Zhen; Wong, Andrew; Kuh, Diana Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1064-3	journal	October 2016
Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type Franco, Irene; Helgadottir, Hafdis T.; Moggio, Aldo Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1892-z	journal	December 2019
Interpreting the dependence of mutation rates on age and time Gao, Ziyue; Wyman, Minyoung J.; Sella, Guy arXiv https://doi.org/10.48550/arxiv.1507.06890	preprint	January 2015
Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis Del Castillo Velasco-Herrera, Martin; van der Weyden, Louise; Nsengimana, Jeremie Molecular Oncology, Vol. 12, Issue 2 https://doi.org/10.1002/1878-0261.12161	journal	January 2018
Next‐Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk Salk, Jesse J.; Kennedy, Scott R. Environmental and Molecular Mutagenesis, Vol. 61, Issue 1 https://doi.org/10.1002/em.22342	journal	November 2019
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal Mitchell, Thomas J.; Turajlic, Samra; Rowan, Andrew Cell, Vol. 173, Issue 3 https://doi.org/10.1016/j.cell.2018.02.020	journal	April 2018
Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis Petljak, Mia; Alexandrov, Ludmil B.; Brammeld, Jonathan S. Cell, Vol. 176, Issue 6 https://doi.org/10.1016/j.cell.2019.02.012	journal	March 2019
Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis Osorio, Fernando G.; Rosendahl Huber, Axel; Oka, Rurika Cell Reports, Vol. 25, Issue 9 https://doi.org/10.1016/j.celrep.2018.11.014	journal	November 2018
Epstein–Barr Virus Infection of Mammary Epithelial Cells Promotes Malignant Transformation Hu, Hai; Luo, Man-Li; Desmedt, Christine EBioMedicine, Vol. 9 https://doi.org/10.1016/j.ebiom.2016.05.025	journal	July 2016
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome Du, Zhenglin; Ma, Liang; Qu, Hongzhu Genomics, Proteomics & Bioinformatics, Vol. 17, Issue 3 https://doi.org/10.1016/j.gpb.2019.07.002	journal	June 2019
Epidermal Darwinism and Competitive Equilibrium within the Epidermis Lei, Mingxing; Chuong, Cheng-Ming Cell Stem Cell, Vol. 23, Issue 5 https://doi.org/10.1016/j.stem.2018.10.019	journal	November 2018
Base changes in tumour DNA have the power to reveal the causes and evolution of cancer Hollstein, M.; Alexandrov, L. B.; Wild, C. P. Oncogene, Vol. 36, Issue 2 https://doi.org/10.1038/onc.2016.192	journal	June 2016
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig Rubanova, Yulia; Shi, Ruian; Harrigan, Caitlin F. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14352-7	journal	February 2020
Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking Cresswell, George D.; Nichol, Daniel; Spiteri, Inmaculada Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15047-9	journal	March 2020
Author Correction: The effects of mutational processes and selection on driver mutations across cancer types Temko, Daniel; Tomlinson, Ian P. M.; Severini, Simone Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15800-0	journal	April 2020
An alternative model for (breast) cancer predisposition Teugels, Erik; De Brakeleer, Sylvia npj Breast Cancer, Vol. 3, Issue 1 https://doi.org/10.1038/s41523-017-0017-7	journal	April 2017
Measuring intratumor heterogeneity by network entropy using RNA-seq data Park, Youngjune; Lim, Sangsoo; Nam, Jin-Wu Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep37767	journal	November 2016
Rational design of non-resistant targeted cancer therapies Martínez-Jiménez, Francisco; Overington, John P.; Al-Lazikani, Bissan Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep46632	journal	April 2017
Complex chromosomal rearrangements by single catastrophic pathogenesis in NUT midline carcinoma Lee, J. -K.; Louzada, S.; An, Y. Annals of Oncology, Vol. 28, Issue 4 https://doi.org/10.1093/annonc/mdw686	journal	April 2017
EGFR mutation subtypes and response to immune checkpoint blockade treatment in non-small-cell lung cancer Hastings, K.; Yu, H. A.; Wei, W. Annals of Oncology, Vol. 30, Issue 8 https://doi.org/10.1093/annonc/mdz141	journal	August 2019
The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes Poulos, Rebecca C.; Olivier, Jake; Wong, Jason W. H. Nucleic Acids Research, Vol. 45, Issue 13 https://doi.org/10.1093/nar/gkx463	journal	May 2017
Somatic Variants in the Human Lens Epithelium: A Preliminary Assessment Mesa, Rosana; Tyagi, Manoj; Harocopos, George Investigative Opthalmology & Visual Science, Vol. 57, Issue 10 https://doi.org/10.1167/iovs.16-19726	journal	August 2016
Single-Cell Analysis Based Dissection of Clonality in Myelofibrosis Mylonas, Elena; Yoshida, Kenichi; Frick, Mareike Blood, Vol. 134, Issue Supplement_1 https://doi.org/10.1182/blood-2019-123367	journal	November 2019
A new timepiece: an epigenetic mitotic clock Christensen, Brock C.; Kelsey, Karl T. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1085-y	journal	October 2016
Exploring the implications of distinct mutational signatures and mutation rates in aging and cancer Fox, Edward J.; Salk, Jesse J.; Loeb, Lawrence A. Genome Medicine, Vol. 8, Issue 1 https://doi.org/10.1186/s13073-016-0286-z	journal	March 2016
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts Saini, Natalie; Roberts, Steven A.; Klimczak, Leszek J. PLOS Genetics, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pgen.1006385	journal	October 2016
Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations Poulos, Rebecca C.; Wong, Yuen T.; Ryan, Regina PLOS Genetics, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pgen.1007779	journal	November 2018
Multipotent Basal Stem Cells, Maintained in Localized Proximal Niches, Support Directed Long-Ranging Epithelial Flows in Human Prostates Moad, M.; Hannezo, E.; Buczacki, Sj Elsevier https://doi.org/10.17863/cam.13421	journalarticle	January 2017
The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils. Stammnitz, Maximilian R.; Coorens, Tim HH; Gori, Kevin C. Elsevier BV https://doi.org/10.17863/cam.21016	journalarticle	January 2018
The ubiquitous ‘cancer mutational signature’ 5 occurs specifically in cancers with deleted FHIT alleles Volinia, Stefano; Druck, Teresa; Paisie, Carolyn A. Oncotarget, Vol. 8, Issue 60 https://doi.org/10.18632/oncotarget.22321	journal	November 2017
Somatic genome alterations in relation to age in lung squamous cell carcinoma Meucci, Stefano; Keilholz, Ulrich; Heim, Daniel Oncotarget, Vol. 9, Issue 63 https://doi.org/10.18632/oncotarget.25848	journal	August 2018
DNA Repair Pathway Alterations in Bladder Cancer Mouw, Kent Cancers, Vol. 9, Issue 12 https://doi.org/10.3390/cancers9040028	journal	March 2017
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity Weiwei, Shi,; Y., Ng, Charlotte K.; S., Lim, Raymond Elsevier https://doi.org/10.5451/unibas-ep68168	text	January 2018
5-hydroxymethylcytosine marks regions with reduced mutation frequency in human DNA Tomkova, Marketa; McClellan, Michael; Kriaucionis, Skirmantas eLife, Vol. 5 https://doi.org/10.7554/elife.17082	journal	May 2016

Similar Records

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

Journal Article · Wed Mar 22 00:00:00 EDT 2017 · Nature (London) · OSTI ID:1236704

Ju, Young Seok; Martincorena, Inigo; Gerstung, Moritz; +38 more

Understanding the origins of human cancer

Journal Article · Fri Dec 04 00:00:00 EST 2015 · Science · OSTI ID:1236704

Alexandrov, L. B.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

Journal Article · Mon May 02 00:00:00 EDT 2016 · Nature (London) · OSTI ID:1236704

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; +85 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
cancer
computational biology and bioinformatics
genomics

Title: Clock-like mutational processes in human somatic cells

Citation Formats

References (30)

Cited By (205)

Similar Records

Related Subjects