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Philip J Stephens,
Patrick S Tarpey,
Helen Davies,
Peter Van Loo,
Chris Greenman,
David C Wedge,
Serena Nik-Zainal,
Sancha Martin, Ignacio Varela,
Graham R Bignell, [......],
Andrew Tutt,
Carlos Caldas,
Jorge S Reis-Filho,
Samuel A J R Aparicio,
Anne Vincent Salomon,
Anne-Lise Børresen-Dale,
Andrea L Richardson,
Peter J Campbell,
P Andrew Futreal,
Michael R Stratton
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ABSTRACT: All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.
Nature 06/2012; 486(7403):400-4. · 36.28 Impact Factor
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Serena Nik-Zainal,
Peter Van Loo,
David C Wedge,
Ludmil B Alexandrov,
Christopher D Greenman,
King Wai Lau,
Keiran Raine,
David Jones,
John Marshall,
Manasa Ramakrishna, [......],
Andrew Tutt,
Anieta M Sieuwerts,
Åke Borg,
Gilles Thomas,
Anne Vincent Salomon,
Andrea L Richardson,
Anne-Lise Børresen-Dale,
P Andrew Futreal,
Michael R Stratton,
Peter J Campbell
[show abstract]
[hide abstract]
ABSTRACT: Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.
Cell 05/2012; 149(5):994-1007. · 32.40 Impact Factor
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Serena Nik-Zainal,
Ludmil B Alexandrov,
David C Wedge,
Peter Van Loo,
Christopher D Greenman,
Keiran Raine,
David Jones,
Jonathan Hinton,
John Marshall,
Lucy A Stebbings, [......],
Samuel A J R Aparicio,
Åke Borg,
Anne Vincent Salomon,
Gilles Thomas,
Anne-Lise Børresen-Dale,
Andrea L Richardson,
Michael S Neuberger,
P Andrew Futreal,
Peter J Campbell,
Michael R Stratton
[show abstract]
[hide abstract]
ABSTRACT: All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed.
Cell 05/2012; 149(5):979-93. · 32.40 Impact Factor
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Ignacio Varela,
Patrick Tarpey,
Keiran Raine,
Dachuan Huang,
Choon Kiat Ong,
Philip Stephens,
Helen Davies,
David Jones,
Meng-Lay Lin,
Jon Teague, [......],
David J Adams,
Alistair Rust,
Waraporn Chan-On,
Chutima Subimerb,
Karl Dykema,
Kyle Furge,
Peter J Campbell,
Bin Tean Teh,
Michael R Stratton,
P Andrew Futreal
Nature 03/2012; · 36.28 Impact Factor
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Kosuke Yusa,
S Tamir Rashid,
Helene Strick-Marchand, Ignacio Varela,
Pei-Qi Liu,
David E Paschon,
Elena Miranda,
Adriana Ordóñez,
Nicholas R F Hannan,
Foad J Rouhani,
Sylvie Darche,
Graeme Alexander,
Stefan J Marciniak,
Noemi Fusaki,
Mamoru Hasegawa,
Michael C Holmes,
James P Di Santo,
David A Lomas,
Allan Bradley,
Ludovic Vallier
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ABSTRACT: Human induced pluripotent stem cells (iPSCs) represent a unique opportunity for regenerative medicine because they offer the prospect of generating unlimited quantities of cells for autologous transplantation, with potential application in treatments for a broad range of disorders. However, the use of human iPSCs in the context of genetically inherited human disease will require the correction of disease-causing mutations in a manner that is fully compatible with clinical applications. The methods currently available, such as homologous recombination, lack the necessary efficiency and also leave residual sequences in the targeted genome. Therefore, the development of new approaches to edit the mammalian genome is a prerequisite to delivering the clinical promise of human iPSCs. Here we show that a combination of zinc finger nucleases (ZFNs) and piggyBac technology in human iPSCs can achieve biallelic correction of a point mutation (Glu342Lys) in the α(1)-antitrypsin (A1AT, also known as SERPINA1) gene that is responsible for α(1)-antitrypsin deficiency. Genetic correction of human iPSCs restored the structure and function of A1AT in subsequently derived liver cells in vitro and in vivo. This approach is significantly more efficient than any other gene-targeting technology that is currently available and crucially prevents contamination of the host genome with residual non-human sequences. Our results provide the first proof of principle, to our knowledge, for the potential of combining human iPSCs with genetic correction to generate clinically relevant cells for autologous cell-based therapies.
Nature 10/2011; 478(7369):391-4. · 36.28 Impact Factor
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Ignacio Varela,
Patrick Tarpey,
Keiran Raine,
Dachuan Huang,
Choon Kiat Ong,
Philip Stephens,
Helen Davies,
David Jones,
Meng-Lay Lin,
Jon Teague, [......],
David J Adams,
Alistair Rust,
Waraporn Chan-on,
Chutima Subimerb,
Karl Dykema,
Kyle Furge,
Peter J Campbell,
Bin Tean Teh,
Michael R Stratton,
P Andrew Futreal
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ABSTRACT: The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ∼3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A), JARID1C (also known as KDM5C) and SETD2 (ref. 2). These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodelling complex gene PBRM1 (ref. 4) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.
Nature 01/2011; 469(7331):539-42. · 36.28 Impact Factor
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Philip J Stephens,
Chris D Greenman,
Beiyuan Fu,
Fengtang Yang,
Graham R Bignell,
Laura J Mudie,
Erin D Pleasance,
King Wai Lau,
David Beare,
Lucy A Stebbings, [......],
Harold Swerdlow,
Nigel P Carter,
Laura A Morsberger,
Christine Iacobuzio-Donahue,
George A Follows,
Anthony R Green,
Adrienne M Flanagan,
Michael R Stratton,
P Andrew Futreal,
Peter J Campbell
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ABSTRACT: Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer.
Cell 01/2011; 144(1):27-40. · 32.40 Impact Factor
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Peter J Campbell,
Shinichi Yachida,
Laura J Mudie,
Philip J Stephens,
Erin D Pleasance,
Lucy A Stebbings,
Laura A Morsberger,
Calli Latimer,
Stuart McLaren,
Meng-Lay Lin, [......],
Andrew Menzies,
Adam P Butler,
Jon W Teague,
Constance A Griffin,
John Burton,
Harold Swerdlow,
Michael A Quail,
Michael R Stratton,
Christine Iacobuzio-Donahue,
P Andrew Futreal
[show abstract]
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ABSTRACT: Pancreatic cancer is an aggressive malignancy with a five-year mortality of 97-98%, usually due to widespread metastatic disease. Previous studies indicate that this disease has a complex genomic landscape, with frequent copy number changes and point mutations, but genomic rearrangements have not been characterized in detail. Despite the clinical importance of metastasis, there remain fundamental questions about the clonal structures of metastatic tumours, including phylogenetic relationships among metastases, the scale of ongoing parallel evolution in metastatic and primary sites, and how the tumour disseminates. Here we harness advances in DNA sequencing to annotate genomic rearrangements in 13 patients with pancreatic cancer and explore clonal relationships among metastases. We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle control, namely dysregulated G1-to-S-phase transition with intact G2-M checkpoint. These initiate amplification of cancer genes and occur predominantly in early cancer development rather than the later stages of the disease. Genomic instability frequently persists after cancer dissemination, resulting in ongoing, parallel and even convergent evolution among different metastases. We find evidence that there is genetic heterogeneity among metastasis-initiating cells, that seeding metastasis may require driver mutations beyond those required for primary tumours, and that phylogenetic trees across metastases show organ-specific branches. These data attest to the richness of genetic variation in cancer, brought about by the tandem forces of genomic instability and evolutionary selection.
Nature 10/2010; 467(7319):1109-13. · 36.28 Impact Factor
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Ignacio Varela,
Christiaan Klijn,
Phillip J Stephens,
Laura J Mudie,
Lucy Stebbings,
Danushka Galappaththige,
Hanneke van der Gulden,
Eva Schut,
Sjoerd Klarenbeek,
Peter J Campbell,
Lodewyk Fa Wessels,
Michael R Stratton,
Jos Jonkers,
P Andrew Futreal,
David J Adams
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ABSTRACT: Here we present the first paired-end sequencing of tumors from genetically engineered mouse models of cancer to determine how faithfully these models recapitulate the landscape of somatic rearrangements found in human tumors. These were models of Trp53-mutated breast cancer, Brca1- and Brca2-associated hereditary breast cancer, and E-cadherin (Cdh1) mutated lobular breast cancer.
We show that although Brca1- and Brca2-deficient mouse mammary tumors have a defect in the homologous recombination pathway, there is no apparent difference in the type or frequency of somatic rearrangements found in these cancers when compared to other mouse mammary cancers, and tumors from all genetic backgrounds showed evidence of microhomology-mediated repair and non-homologous end-joining processes. Importantly, mouse mammary tumors were found to carry fewer structural rearrangements than human mammary cancers and expressed in-frame fusion genes. Like the fusion genes found in human mammary tumors, these were not recurrent. One mouse tumor was found to contain an internal deletion of exons of the Lrp1b gene, which led to a smaller in-frame transcript. We found internal in-frame deletions in the human ortholog of this gene in a significant number (4.2%) of human cancer cell lines.
Paired-end sequencing of mouse mammary tumors revealed that they display significant heterogeneity in their profiles of somatic rearrangement but, importantly, fewer rearrangements than cognate human mammary tumors, probably because these cancers have been induced by strong driver mutations engineered into the mouse genome. Both human and mouse mammary cancers carry expressed fusion genes and conserved homozygous deletions.
Genome biology 10/2010; 11(10):R100. · 6.63 Impact Factor
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Philip J Stephens,
David J McBride,
Meng-Lay Lin, Ignacio Varela,
Erin D Pleasance,
Jared T Simpson,
Lucy A Stebbings,
Catherine Leroy,
Sarah Edkins,
Laura J Mudie, [......],
Anita Langerød,
Hege E G Russnes,
John A Foekens,
Jorge S Reis-Filho,
Laura van 't Veer,
Andrea L Richardson,
Anne-Lise Børresen-Dale,
Peter J Campbell,
P Andrew Futreal,
Michael R Stratton
[show abstract]
[hide abstract]
ABSTRACT: Multiple somatic rearrangements are often found in cancer genomes; however, the underlying processes of rearrangement and their contribution to cancer development are poorly characterized. Here we use a paired-end sequencing strategy to identify somatic rearrangements in breast cancer genomes. There are more rearrangements in some breast cancers than previously appreciated. Rearrangements are more frequent over gene footprints and most are intrachromosomal. Multiple rearrangement architectures are present, but tandem duplications are particularly common in some cancers, perhaps reflecting a specific defect in DNA maintenance. Short overlapping sequences at most rearrangement junctions indicate that these have been mediated by non-homologous end-joining DNA repair, although varying sequence patterns indicate that multiple processes of this type are operative. Several expressed in-frame fusion genes were identified but none was recurrent. The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development.
Nature 12/2009; 462(7276):1005-10. · 36.28 Impact Factor
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Erin D Pleasance,
Philip J Stephens,
Sarah O'Meara,
David J McBride,
Alison Meynert,
David Jones,
Meng-Lay Lin,
David Beare,
King Wai Lau,
Chris Greenman, [......],
Gina L Costa,
Clarence C Lee,
John D Minna,
Adi Gazdar,
Ewan Birney,
Michael D Rhodes,
Kevin J McKernan,
Michael R Stratton,
P Andrew Futreal,
Peter J Campbell
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ABSTRACT: Cancer is driven by mutation. Worldwide, tobacco smoking is the principal lifestyle exposure that causes cancer, exerting carcinogenicity through >60 chemicals that bind and mutate DNA. Using massively parallel sequencing technology, we sequenced a small-cell lung cancer cell line, NCI-H209, to explore the mutational burden associated with tobacco smoking. A total of 22,910 somatic substitutions were identified, including 134 in coding exons. Multiple mutation signatures testify to the cocktail of carcinogens in tobacco smoke and their proclivities for particular bases and surrounding sequence context. Effects of transcription-coupled repair and a second, more general, expression-linked repair pathway were evident. We identified a tandem duplication that duplicates exons 3-8 of CHD7 in frame, and another two lines carrying PVT1-CHD7 fusion genes, indicating that CHD7 may be recurrently rearranged in this disease. These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer.
Nature 12/2009; 463(7278):184-90. · 36.28 Impact Factor
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Erin D Pleasance,
R Keira Cheetham,
Philip J Stephens,
David J McBride,
Sean J Humphray,
Chris D Greenman, Ignacio Varela,
Meng-Lay Lin,
Gonzalo R Ordóñez,
Graham R Bignell, [......],
Lucy A Stebbings,
Lukasz Szajkowski,
Jon Teague,
David Williamson,
Lynda Chin,
Mark T Ross,
Peter J Campbell,
David R Bentley,
P Andrew Futreal,
Michael R Stratton
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[hide abstract]
ABSTRACT: All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.
Nature 12/2009; 463(7278):191-6. · 36.28 Impact Factor
