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

Abstract

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.

Authors:

^[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)

Publication Date:: Mon Nov 09 00:00:00 EST 2015

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

Sponsoring Org.:: USDOE

OSTI Identifier:: 1236704

Report Number(s):: LA-UR-15-21254
Journal ID: ISSN 1061-4036; ng.3441

Grant/Contract Number:: AC52-06NA25396

Resource Type:: Accepted Manuscript

Journal Name:: Nature Genetics

Additional Journal Information:: Journal Volume: 47; Journal Issue: 12; Journal ID: ISSN 1061-4036

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; cancer; computational biology and bioinformatics; genomics

Citation Formats


                    Alexandrov, Ludmil B., Jones, Philip H., Wedge, David C., Sale, Julian E., Campbell, Peter J., Nik-Zainal, Serena, and Stratton, Michael R. Clock-like mutational processes in human somatic cells.  United States: N. p., 2015. 
Web.  doi:10.1038/ng.3441.

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                    Alexandrov, Ludmil B., Jones, Philip H., Wedge, David C., Sale, Julian E., Campbell, Peter J., Nik-Zainal, Serena, & Stratton, Michael R. Clock-like mutational processes in human somatic cells.  United States.  https://doi.org/10.1038/ng.3441

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                    Alexandrov, Ludmil B., Jones, Philip H., Wedge, David C., Sale, Julian E., Campbell, Peter J., Nik-Zainal, Serena, and Stratton, Michael R. Mon .  
"Clock-like mutational processes in human somatic cells".  United States.  https://doi.org/10.1038/ng.3441.  https://www.osti.gov/servlets/purl/1236704.

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@article{osti_1236704,

  title        = {Clock-like mutational processes in human somatic cells},

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

  abstractNote = {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.},

  doi          = {10.1038/ng.3441},

  journal      = {Nature Genetics},

  number       = 12,

  volume       = 47,

  place        = {United States},

  year         = {Mon Nov 09 00:00:00 EST 2015},

  month        = {Mon Nov 09 00:00:00 EST 2015}

}

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Title: Clock-like mutational processes in human somatic cells

Abstract

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Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues journal, May 2016

Integrative genomic analysis of mouse and human hepatocellular carcinoma journal, October 2018

Pancreatic cancer organoids recapitulate disease and allow personalized drug screening journal, December 2019

Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations journal, December 2019

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer journal, June 2017

Modeling clinical and molecular covariates of mutational process activity in cancer journal, July 2019

The cancer genome
journal, April 2009

Mutational signatures: the patterns of somatic mutations hidden in cancer genomes
journal, February 2014

Mechanisms underlying mutational signatures in human cancers
journal, July 2014

Signatures of mutational processes in human cancer
journal, August 2013

Mutational Processes Molding the Genomes of 21 Breast Cancers
journal, May 2012

Deciphering Signatures of Mutational Processes Operative in Human Cancer
journal, January 2013

DNA Replication in Eukaryotic Cells
journal, June 2002

DNA methylation age of human tissues and cell types
journal, January 2013

Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects
journal, January 2008

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
journal, September 2014

The Origin and Evolution of Mutations in Acute Myeloid Leukemia
journal, July 2012

Rate of de novo mutations and the importance of father’s age to disease risk
journal, August 2012

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation
journal, December 2012

Variation in genome-wide mutation rates within and between human families
journal, June 2011

Genome sequencing of normal cells reveals developmental lineages and mutational processes
journal, June 2014

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma
journal, January 2014

Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage
journal, January 2014

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer
journal, April 2014

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing
journal, February 2014

Subclonal diversification of primary breast cancer revealed by multiregion sequencing
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
journal, February 2015

Robust regression using iteratively reweighted least-squares
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Robust Statistics
book, January 2009

On a Robust Correlation Coefficient
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Disease-associated DNA methylation signatures in esophageal biopsies of children diagnosed with Eosinophilic Esophagitis
journal, April 2021

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.
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Deciphering signatures of mutational processes operative in human cancer.
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Signatures of mutational processes in human cancer.
text, January 2013

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer.
text, January 2014

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
text, January 2014

Mechanisms underlying mutational signatures in human cancers
journal, July 2014

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
journal, March 2020

Cancer etiology: Variation in cancer risk among tissues is poorly explained by the number of gene mutations
journal, February 2018

Most gene fusions in cancer are stochastic events
journal, March 2019

Integrative genomic analysis identifies associations of molecular alterations to APOBEC and BRCA1/2 mutational signatures in breast cancer
journal, June 2019

Mutational signature analysis identifies MUTYH deficiency in colorectal cancers and adrenocortical carcinomas: Mutational signature associated with MUTYH deficiency in cancers
journal, March 2017

Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma
journal, August 2019

Nucleotide Excision Repair: From Neurodegeneration to Cancer
book, January 2017

Genomics and clinical correlates of renal cell carcinoma
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Somatic mutations in neurons during aging and neurodegeneration
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The role of DNA damage as a therapeutic target in autosomal dominant polycystic kidney disease
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The landscape of genomic alterations across childhood cancers
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Analysis of cancer genomes reveals basic features of human aging and its role in cancer development
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Differences between germline and somatic mutation rates in humans and mice
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Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors
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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
journal, May 2016

An evolutionary perspective on field cancerization
journal, December 2017

Clonal evolution of colorectal cancer in IBD
journal, February 2017

APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma
journal, January 2019

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
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The effects of mutational processes and selection on driver mutations across cancer types
journal, May 2018

Genomic patterns of progression in smoldering multiple myeloma
journal, August 2018

Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma
journal, January 2019

Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma
journal, April 2019

ALPK1 hotspot mutation as a driver of human spiradenoma and spiradenocarcinoma
journal, May 2019

Brain somatic mutations observed in Alzheimer’s disease associated with aging and dysregulation of tau phosphorylation
journal, July 2019

Genomic landscape and chronological reconstruction of driver events in multiple myeloma
journal, August 2019

Integrated exome and RNA sequencing of dedifferentiated liposarcoma
journal, December 2019

Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer
journal, January 2020

The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly
journal, January 2020

Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
journal, August 2018

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours
journal, November 2018

Intra-tumour diversification in colorectal cancer at the single-cell level
journal, April 2018

The repertoire of mutational signatures in human cancer
journal, February 2020

DNA methylation loss in late-replicating domains is linked to mitotic cell division
journal, April 2018

Detecting the mutational signature of homologous recombination deficiency in clinical samples
journal, April 2019

The mutational footprints of cancer therapies
journal, November 2019

Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma
journal, January 2020

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions
journal, January 2019

Genomic features of renal cell carcinoma with venous tumor thrombus
journal, May 2018

Burden of unique and low prevalence somatic mutations correlates with cancer survival
journal, March 2019

Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues
journal, May 2016

Integrative genomic analysis of mouse and human hepatocellular carcinoma
journal, October 2018

Pancreatic cancer organoids recapitulate disease and allow personalized drug screening
journal, December 2019

Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations
journal, December 2019

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer
journal, June 2017

Modeling clinical and molecular covariates of mutational process activity in cancer
journal, July 2019

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26
journal, February 2017

Neutral Theory and the Somatic Evolution of Cancer
journal, April 2018

Mutations Beget More Mutations—Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation
journal, December 2019