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ABSTRACT: Subclones homozygous for JAK2V617F are more common and larger in patients with polycythemia vera compared to essential thrombocythemia, but their role in determining phenotype remains unclear. We genotyped 4564 erythroid colonies from 59 patients with polycythemia vera or essential thrombocythemia to investigate whether the proportion of JAK2V617F -homozygous precursors, compared to heterozygous precursors, is associated with clinical or demographic features. In polycythemia vera, a higher proportion of homozygous-mutant precursors was associated with more extreme blood counts at diagnosis, consistent with a causal role for homozygosity in polycythemia vera pathogenesis. Larger numbers of homozygous-mutant colonies were associated with older age, and with male gender in polycythemia vera but female gender in essential thrombocythemia. These results suggest that age promotes development or expansion of homozygous-mutant clones and that gender modulates the phenotypic consequences of JAK2V617F homozygosity, thus providing a potential explanation for the long-standing observations of a preponderance of men with polycythemia vera but of women with essential thrombocythemia.
Haematologica 05/2013; 98(5):718-21. · 6.42 Impact Factor
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ABSTRACT: The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific opportunity for different mutation types according to sequence composition. Applying EMu to breast cancer data, we derive detailed maps of the activity of each process, both genome-wide and within specific local regions of the genome. Our work provides new opportunities to study the mutational processes underlying cancer development. EMu is available at http://www.sanger.ac.uk/resources/software/emu/.
Genome biology 04/2013; 14(4):R39. · 6.63 Impact Factor
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Thierry Voet,
Parveen Kumar,
Peter Van Loo,
Susanna L Cooke,
John Marshall,
Meng-Lay Lin,
Masoud Zamani Esteki,
Niels Van der Aa,
Ligia Mateiu,
David J McBride, [......],
Adam Butler,
Keiran Raine,
Lucy A Stebbings,
Michael A Quail,
Thomas D'Hooghe,
Yves Moreau,
P Andrew Futreal,
Michael R Stratton,
Joris R Vermeesch, Peter J Campbell
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ABSTRACT: The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.
Nucleic Acids Research 04/2013; · 8.03 Impact Factor
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Athar Aziz,
E Joanna Baxter,
Carol Edwards,
Clara Yujing Cheong,
Mitsuteru Ito,
Anthony Bench,
Rebecca Kelley,
Yvonne Silber,
Philip A Beer,
Keefe Chng, [......],
Kirsten McEwen,
Dionne Gray,
Jyoti Nangalia,
Ghulam J Mufti,
Eva Hellstrom-Lindberg,
Jean-Jacques Kiladjian,
Mary Frances McMullin, Peter J Campbell,
Anne C Ferguson-Smith,
Anthony R Green
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ABSTRACT: Large regions of recurrent genomic loss are common in cancers; however, with a few well-characterized exceptions, how they contribute to tumor pathogenesis remains largely obscure. Here we identified primate-restricted imprinting of a gene cluster on chromosome 20 in the region commonly deleted in chronic myeloid malignancies. We showed that a single heterozygous 20q deletion consistently resulted in the complete loss of expression of the imprinted genes L3MBTL1 and SGK2, indicative of a pathogenetic role for loss of the active paternally inherited locus. Concomitant loss of both L3MBTL1 and SGK2 dysregulated erythropoiesis and megakaryopoiesis, 2 lineages commonly affected in chronic myeloid malignancies, with distinct consequences in each lineage. We demonstrated that L3MBTL1 and SGK2 collaborated in the transcriptional regulation of MYC by influencing different aspects of chromatin structure. L3MBTL1 is known to regulate nucleosomal compaction, and we here showed that SGK2 inactivated BRG1, a key ATP-dependent helicase within the SWI/SNF complex that regulates nucleosomal positioning. These results demonstrate a link between an imprinted gene cluster and malignancy, reveal a new pathogenetic mechanism associated with acquired regions of genomic loss, and underline the complex molecular and cellular consequences of "simple" cancer-associated chromosome deletions.
The Journal of clinical investigation 04/2013; · 15.39 Impact Factor
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ABSTRACT: The genome of a cancer cell carries somatic mutations that are the cumulative consequences of the DNA damage and repair processes operative during the cellular lineage between the fertilized egg and the cancer cell. Remarkably, these mutational processes are poorly characterized. Global sequencing initiatives are yielding catalogs of somatic mutations from thousands of cancers, thus providing the unique opportunity to decipher the signatures of mutational processes operative in human cancer. However, until now there have been no theoretical models describing the signatures of mutational processes operative in cancer genomes and no systematic computational approaches are available to decipher these mutational signatures. Here, by modeling mutational processes as a blind source separation problem, we introduce a computational framework that effectively addresses these questions. Our approach provides a basis for characterizing mutational signatures from cancer-derived somatic mutational catalogs, paving the way to insights into the pathogenetic mechanism underlying all cancers.
Cell reports. 01/2013;
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Ilaria Ambaglio,
Luca Malcovati,
Elli Papaemmanuil,
Coby M Laarakkers,
Matteo G Della Porta,
Anna Galli,
Matteo C Da Via,
Elisa Bono,
Marta Ubezio,
Erica Travaglino,
Riccardo Albertini, Peter J Campbell,
Dorine W Swinkels,
Mario Cazzola
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ABSTRACT: Somatic mutations of the RNA splicing machinery have been recently identified in myelodysplastic syndromes (MDS). In particular, a strong association has been found between SF3B1 mutation and refractory anemia with ring sideroblasts, a condition characterized by ineffective erythropoiesis and parenchymal iron overload. We studied the relationship between SF3B1 mutation, erythroid activity and hepcidin levels in MDS patients. Erythroid activity was evaluated through the proportion of marrow erythroblasts, soluble transferrin receptor (sTfR) and serum growth differentiation factor 15 (GDF15). Significant relationships were found between SF3B1 mutation and marrow erythroblasts (P=.001), sTfR (P=.003) or serum GDF15 (P=.033). Serum hepcidin varied considerably, and multivariable analysis showed that the hepcidin to ferritin ratio, a measure of adequacy of hepcidin levels relative to body iron stores, was inversely related to the SF3B1 mutation (P=.013). These observations suggest that patients with SF3B1 mutation have inappropriately low hepcidin levels, which may explain their propensity to parenchymal iron loading.
Haematologica 01/2013; · 6.42 Impact Factor
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ABSTRACT: Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions, often associated with sites of DNA rearrangement. We show kataegis can result from AID/APOBEC-catalysed cytidine deamination in the vicinity of DNA breaks, likely through action on single-stranded DNA exposed during resection. Cancer-like kataegis can be recapitulated by expression of AID/APOBEC family deaminases in yeast where it largely depends on uracil excision, which generates an abasic site for strand breakage. Localized kataegis can also be nucleated by an I-SceI-induced break. Genome-wide patterns of APOBEC3-catalyzed deamination in yeast reveal APOBEC3B and 3A as the deaminases whose mutational signatures are most similar to those of breast cancer kataegic mutations. Together with expression and functional assays, the results implicate APOBEC3B/A in breast cancer hypermutation and give insight into the mechanism of kataegis. DOI:http://dx.doi.org/10.7554/eLife.00534.001.
eLife. 01/2013; 2:e00534.
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Rocco Piazza,
Simona Valletta,
Nils Winkelmann,
Sara Redaelli,
Roberta Spinelli,
Alessandra Pirola,
Laura Antolini,
Luca Mologni,
Carla Donadoni,
Elli Papaemmanuil, [......],
Valeria Fantin,
Graham R Bignell,
Vera Magistroni,
Torsten Haferlach,
Enrico Maria Pogliani, Peter J Campbell,
Andrew J Chase,
William J Tapper,
Nicholas C P Cross,
Carlo Gambacorti-Passerini
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ABSTRACT: Atypical chronic myeloid leukemia (aCML) shares clinical and laboratory features with CML, but it lacks the BCR-ABL1 fusion. We performed exome sequencing of eight aCMLs and identified somatic alterations of SETBP1 (encoding a p.Gly870Ser alteration) in two cases. Targeted resequencing of 70 aCMLs, 574 diverse hematological malignancies and 344 cancer cell lines identified SETBP1 mutations in 24 cases, including 17 of 70 aCMLs (24.3%; 95% confidence interval (CI) = 16-35%). Most mutations (92%) were located between codons 858 and 871 and were identical to changes seen in individuals with Schinzel-Giedion syndrome. Individuals with mutations had higher white blood cell counts (P = 0.008) and worse prognosis (P = 0.01). The p.Gly870Ser alteration abrogated a site for ubiquitination, and cells exogenously expressing this mutant exhibited higher amounts of SETBP1 and SET protein, lower PP2A activity and higher proliferation rates relative to those expressing the wild-type protein. In summary, mutated SETBP1 represents a newly discovered oncogene present in aCML and closely related diseases.
Nature Genetics 12/2012; · 35.53 Impact Factor
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ABSTRACT: The advent of massively parallel sequencing technologies has allowed the characterization of cancer genomes at an unprecedented resolution. Investigation of the mutational landscape of tumours is providing new insights into cancer genome evolution, laying bare the interplay of somatic mutation, adaptation of clones to their environment and natural selection. These studies have demonstrated the extent of the heterogeneity of cancer genomes, have allowed inferences to be made about the forces that act on nascent cancer clones as they evolve and have shown insight into the mutational processes that generate genetic variation. Here we review our emerging understanding of the dynamic evolution of the cancer genome and of the implications for basic cancer biology and the development of antitumour therapy.
Nature Reviews Genetics 10/2012; 13(11):795-806. · 38.08 Impact Factor
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ABSTRACT: We are currently on the threshold of a revolution in breast cancer research, thanks to the emergence of novel technologies based on next-generation sequencing (NGS). In this review, we will describe the different sequencing technologies and platforms, and summarize the main findings from the latest sequencing articles in breast cancer.
Firstly, the sequencing of a few hundreds of breast tumors has revealed new cancer genes. Although these were not frequently mutated, mutated genes from different patients could be grouped into the deregulation of similar pathways. Secondly, NGS allowed further exploration of intratumor heterogeneity and revealed that although subclonal mutations were present in all tumors, there was always a dominant clone, which comprised at least 50% of the tumor cells. Finally, tumor-specific DNA rearrangements could be detected in the patient's plasma, suggesting that NGS could be used to personalize the monitoring of the disease.
The application of NGS to breast cancer has been associated with tremendous advances and promises for increasing the understanding of the disease. However, there still remain many unanswered questions, such as the role of structural changes of tumor genomes in cancer progression and treatment response/resistance.
Current opinion in oncology 09/2012; 24(6):597-604. · 4.09 Impact Factor
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Anna L Godfrey,
Edwin Chen,
Francesca Pagano,
Christina A Ortmann,
Yvonne Silber,
Beatriz Bellosillo,
Paola Guglielmelli,
Claire N Harrison,
John T Reilly,
Frank Stegelmann,
Fontanet Bijou,
Eric Lippert,
Mary F McMullin,
Jean-Michel Boiron,
Konstanze Döhner,
Alessandro M Vannucchi,
Carlos Besses, Peter J Campbell,
Anthony R Green
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ABSTRACT: Subclones homozygous for JAK2V617F are more common in polycythemia vera (PV) than essential thrombocythemia (ET), but their prevalence and significance remain unclear. The JAK2 mutation status of 6495 BFU-E, grown in low erythropoietin conditions, was determined in 77 patients with PV or ET. Homozygous-mutant colonies were common in patients with JAK2V617F-positive PV and were surprisingly prevalent in JAK2V617F-positive ET and JAK2 exon 12-mutated PV. Using microsatellite PCR to map loss-of-heterozygosity breakpoints within individual colonies, we demonstrate that recurrent acquisition of JAK2V617F homozygosity occurs frequently in both PV and ET. PV was distinguished from ET by expansion of a dominant homozygous subclone, the selective advantage of which is likely to reflect additional genetic or epigenetic lesions. Our results suggest a model in which development of a dominant JAK2V617F-homzygous subclone drives erythrocytosis in many PV patients, with alternative mechanisms operating in those with small or undetectable homozygous-mutant clones.
Blood 08/2012; 120(13):2704-7. · 9.90 Impact Factor
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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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ABSTRACT: Essential thrombocythemia, a myeloproliferative neoplasm, is associated with increased platelet count and risk of thrombosis or hemorrhage. Cytoreductive therapy aims to normalize platelet counts despite there being only a minimal association between platelet count and complication rates. Evidence is increasing for a correlation between WBC count and thrombosis, but prospective data are lacking. In the present study, we investigated the relationship between vascular complications and 21 887 longitudinal blood counts in a prospective, multicenter cohort of 776 essential thrombocythemia patients. After correction for confounding variables, no association was seen between blood counts at diagnosis and future complications. However, platelet count outside of the normal range during follow-up was associated with an immediate risk of major hemorrhage (P = .0005) but not thrombosis (P = .7). Elevated WBC count during follow-up was correlated with thrombosis (P = .05) and major hemorrhage (P = .01). These data imply that the aim of cytoreduction in essential thrombocythemia should be to keep the platelet count, and arguably the WBC count, within the normal range. This study is registered at the International Standard Randomized Controlled Trials Number Registry (www.isrctn.org) as number 72251782.
Blood 06/2012; 120(7):1409-11. · 9.90 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
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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
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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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David J McBride,
Dariush Etemadmoghadam,
Susanna L Cooke,
Kathryn Alsop,
Joshy George,
Adam Butler,
Juok Cho,
Danushka Galappaththige,
Chris Greenman,
Karen D Howarth, [......],
Keiran Raine,
Jon Teague,
David C Wedge,
Australian Ovarian Cancer Study Group,
Xavier Caubit,
Michael R Stratton,
James D Brenton, Peter J Campbell,
P Andrew Futreal,
David Dl Bowtell
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ABSTRACT: The application of paired-end next generation sequencing approaches has made it possible to systematically characterize rearrangements of the cancer genome to base-pair level. Utilizing this approach, we report the first detailed analysis of ovarian cancer rearrangements, comparing high-grade serous and clear cell cancers, and these histotypes with other solid cancers. Somatic rearrangements were systematically characterized in eight high-grade serous and five clear cell ovarian cancer genomes and we report here the identification of > 600 somatic rearrangements. Recurrent rearrangements of the transcriptional regulator gene, TSHZ3, were found in three of eight serous cases. Comparison to breast, pancreatic and prostate cancer genomes revealed that a subset of ovarian cancers share a marked tandem duplication phenotype with triple-negative breast cancers. The tandem duplication phenotype was not linked to BRCA1/2 mutation, suggesting that other common mechanisms or carcinogenic exposures are operative. High-grade serous cancers arising in women with germline BRCA1 or BRCA2 mutation showed a high frequency of small chromosomal deletions. These findings indicate that BRCA1/2 germline mutation may contribute to widespread structural change and that other undefined mechanism(s), which are potentially shared with triple-negative breast cancer, promote tandem chromosomal duplications that sculpt the ovarian cancer genome.
The Journal of Pathology 04/2012; 227(4):446-55. · 6.32 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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Elizabeth P Murchison,
Ole B Schulz-Trieglaff,
Zemin Ning,
Ludmil B Alexandrov,
Markus J Bauer,
Beiyuan Fu,
Matthew Hims,
Zhihao Ding,
Sergii Ivakhno,
Caitlin Stewart, [......],
Kevin Hall,
Stephen M J Searle,
Nigel P Carter,
Anthony T Papenfuss,
P Andrew Futreal, Peter J Campbell,
Fengtang Yang,
David R Bentley,
Dirk J Evers,
Michael R Stratton
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ABSTRACT: The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.
Cell 02/2012; 148(4):780-91. · 32.40 Impact Factor
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Chris D Greenman,
Erin D Pleasance,
Scott Newman,
Fengtang Yang,
Beiyuan Fu,
Serena Nik-Zainal,
David Jones,
King Wai Lau,
Nigel Carter,
Paul A W Edwards,
P Andrew Futreal,
Michael R Stratton, Peter J Campbell
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ABSTRACT: Cancer genomes are complex, carrying thousands of somatic mutations including base substitutions, insertions and deletions, rearrangements, and copy number changes that have been acquired over decades. Recently, technologies have been introduced that allow generation of high-resolution, comprehensive catalogs of somatic alterations in cancer genomes. However, analyses of these data sets generally do not indicate the order in which mutations have occurred, or the resulting karyotype. Here, we introduce a mathematical framework that begins to address this problem. By using samples with accurate data sets, we can reconstruct relatively complex temporal sequences of rearrangements and provide an assembly of genomic segments into digital karyotypes. For cancer genes mutated in rearranged regions, this information can provide a chronological examination of the selective events that have taken place.
Genome Research 02/2012; 22(2):346-61. · 13.61 Impact Factor
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Nature Biotechnology 01/2012; 30(7):620-1. · 29.50 Impact Factor
