2010年12月14日火曜日

様々な癌腫の変異リスト：関連する参考文献

8月に出た癌の突然変異：様々な癌腫の変異リスト・・この論文に関連する参考文献としてnature誌が挙げた50編の論文リストをノートしておく。




Diverse somatic mutation patterns and pathway alterations in human cancers

Nature　　Volume:466,　Pages:869–873　Date published:(12 August 2010)

  1. Somatic mutations affect key pathways in lung adenocarcinoma

    Nature 455, 1069–1075 (2008) 10.1038/nature07423

  2. Advances in understanding cancer genomes through second-generation sequencing

    • Matthew Meyerson,
    • Stacey Gabriel
    • & Gad Getz

    Nature Reviews Genetics 11, 685–696 (2010) 10.1038/nrg2841

  3. The mutation spectrum revealed by paired genome sequences from a lung cancer patient

    • William Lee,
    • Zhaoshi Jiang,
    • Jinfeng Liu,
    • Peter M. Haverty,
    • Yinghui Guan,
    • Jeremy Stinson
    • Peng Yue,
    • Yan Zhang,
    • Krishna P. Pant,
    • Deepali Bhatt,
    • Connie Ha,
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    • Michael I. Kennemer,
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    • Igor Nazarenko,
    • Colin Watanabe,
    • Andrew B. Sparks,
    • David S. Shames,
    • Robert Gentleman,
    • Frederic J. de Sauvage,
    • Howard Stern,
    • Ajay Pandita,
    • Dennis G. Ballinger,
    • Radoje Drmanac,
    • Zora Modrusan,

    Nature 465, 473–477 (2010) 10.1038/nature09004

  4. Genome remodelling in a basal-like breast cancer metastasis and xenograft

    • Li Ding,
    • Matthew J. Ellis,
    • Shunqiang Li,
    • David E. Larson,
    • Ken Chen,
    • John W. Wallis
    • Christopher C. Harris,
    • Michael D. McLellan,
    • Robert S. Fulton,
    • Lucinda L. Fulton,
    • Rachel M. Abbott,
    • Jeremy Hoog,
    • David J. Dooling,
    • Daniel C. Koboldt,
    • Heather Schmidt,
    • Joelle Kalicki,
    • Qunyuan Zhang,
    • Lei Chen,
    • Ling Lin,
    • Michael C. Wendl,
    • Joshua F. McMichael,
    • Vincent J. Magrini,
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    • Sean D. McGrath,
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    • Elizabeth Appelbaum,
    • Katherine DeSchryver,
    • Sherri Davies,
    • Therese Guintoli,
    • Li Lin,
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    • Yu Tao,
    • Jacqueline E. Snider,
    • Scott M. Smith,
    • Adam F. Dukes,
    • Gabriel E. Sanderson,
    • Craig S. Pohl,
    • Kim D. Delehaunty,
    • Catrina C. Fronick,
    • Kimberley A. Pape,
    • Jerry S. Reed,
    • Jody S. Robinson,
    • Jennifer S. Hodges,
    • William Schierding,
    • Nathan D. Dees,
    • Dong Shen,
    • Devin P. Locke,
    • Madeline E. Wiechert,
    • James M. Eldred,
    • Josh B. Peck,
    • Benjamin J. Oberkfell,
    • Justin T. Lolofie,
    • Feiyu Du,
    • Amy E. Hawkins,
    • Michelle D. O’Laughlin,
    • Kelly E. Bernard,
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    • Dominic M. Thompson Jr,
    • Jennifer L. Ivanovich,
    • Paul J. Goodfellow,
    • Charles M. Perou,
    • George M. Weinstock,
    • Rebecca Aft,
    • Mark Watson,
    • Timothy J. Ley,

    Nature 464, 999–1005 (2010) 10.1038/nature08989

  5. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    Nature 455, 1061–1068 (2008) 10.1038/nature07385

  6. Patterns of somatic mutation in human cancer genomes

    • Christopher Greenman,
    • Philip Stephens,
    • Raffaella Smith,
    • Gillian L. Dalgliesh,
    • Christopher Hunter,
    • Graham Bignell
    • Helen Davies,
    • Jon Teague,
    • Adam Butler,
    • Claire Stevens,
    • Sarah Edkins,
    • Sarah O’Meara,
    • Imre Vastrik,
    • Esther E. Schmidt,
    • Tim Avis,
    • Syd Barthorpe,
    • Gurpreet Bhamra,
    • Gemma Buck,
    • Bhudipa Choudhury,
    • Jody Clements,
    • Jennifer Cole,
    • Ed Dicks,
    • Simon Forbes,
    • Kris Gray,
    • Kelly Halliday,
    • Rachel Harrison,
    • Katy Hills,
    • Jon Hinton,
    • Andy Jenkinson,
    • David Jones,
    • Andy Menzies,
    • Tatiana Mironenko,
    • Janet Perry,
    • Keiran Raine,
    • Dave Richardson,
    • Rebecca Shepherd,
    • Alexandra Small,
    • Calli Tofts,
    • Jennifer Varian,
    • Tony Webb,
    • Sofie West,
    • Sara Widaa,
    • Andy Yates,
    • Daniel P. Cahill,
    • David N. Louis,
    • Peter Goldstraw,
    • Andrew G. Nicholson,
    • Francis Brasseur,
    • Leendert Looijenga,
    • Barbara L. Weber,
    • Yoke-Eng Chiew,
    • Anna deFazio,
    • Mel F. Greaves,
    • Anthony R. Green,
    • Peter Campbell,
    • Ewan Birney,
    • Douglas F. Easton,
    • Georgia Chenevix-Trench,
    • Min-Han Tan,
    • Sok Kean Khoo,
    • Bin Tean Teh,
    • Siu Tsan Yuen,
    • Suet Yi Leung,
    • Richard Wooster,

    Nature 446, 153–158 (2007) 10.1038/nature05610

  7. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors

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    • L Wang,
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    • M F Zakowski,
    • V Rusch,
    • W Pao,

    Oncogene 28, 2773–2783 (2009) 10.1038/onc.2009.135

  8. The GPCR-cancer connection

    • Joanne Kotz

    Science-Business eXchange 3 (2010) 10.1038/scibx.2010.942

  9. The cancer genome

    • Michael R. Stratton,
    • Peter J. Campbell
    • & P. Andrew Futreal

    Nature 458, 719–724 (2009) 10.1038/nature07943

  10. High-resolution mapping of copy-number alterations with massively parallel sequencing

    • Derek Y Chiang,
    • Gad Getz,
    • David B Jaffe,
    • Michael J T O'Kelly,
    • Xiaojun Zhao,
    • Scott L Carter
    • Carsten Russ,
    • Chad Nusbaum,

    Nature Methods 6, 99–103 (2008) 10.1038/nmeth.1276

  11. A comprehensive catalogue of somatic mutations from a human cancer genome

    • P. Andrew Futreal
    • Michael R. Stratton

    Nature 463, 191–196 (2009) 10.1038/nature08658

  12. Genomic characterization of asymtpomatic CT-detected lung cancers

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    • G Taliento,
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    Oncogene (2010) 10.1038/onc.2010.478

  13. A census of human cancer genes

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    • Lachlan Coin,
    • Mhairi Marshall,
    • Thomas Down,
    • Timothy Hubbard,
    • Richard Wooster

    Nature Reviews Cancer 4, 177–183 (2004) 10.1038/nrc1299

  14. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers

    • Richard S. Maser,
    • Bhudipa Choudhury,
    • Peter J. Campbell,
    • Bin Feng,
    • Kwok-Kin Wong,
    • Alexei Protopopov
    • Jennifer O’Neil,
    • Alejandro Gutierrez,
    • Elena Ivanova,
    • Ilana Perna,
    • Eric Lin,
    • Vidya Mani,
    • Shan Jiang,
    • Kate McNamara,
    • Sara Zaghlul,
    • Sarah Edkins,
    • Claire Stevens,
    • Cameron Brennan,
    • Eric S. Martin,
    • Ruprecht Wiedemeyer,
    • Omar Kabbarah,
    • Cristina Nogueira,
    • Gavin Histen,
    • Jon Aster,
    • Marc Mansour,
    • Veronique Duke,
    • Letizia Foroni,
    • Adele K. Fielding,
    • Anthony H. Goldstone,
    • Jacob M. Rowe,
    • Yaoqi A. Wang,
    • A. Thomas Look,
    • Michael R. Stratton,
    • Lynda Chin,

    Nature 447, 966–971 (2007) 10.1038/nature05886

  15. Mutated genes, pathways and processes in tumours

    • Anaïs Baudot,
    • Victor de la Torre
    • & Alfonso Valencia

    EMBO reports 11, 805–810 (2010) 10.1038/embor.2010.133

  16. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

    • Ryan D Morin,
    • Nathalie A Johnson,
    • Tesa M Severson,
    • Andrew J Mungall,
    • Jianghong An,
    • Rodrigo Goya
    • Jessica E Paul,
    • Merrill Boyle,
    • Bruce W Woolcock,
    • Florian Kuchenbauer,
    • Damian Yap,
    • R Keith Humphries,
    • Obi L Griffith,
    • Sohrab Shah,
    • Henry Zhu,
    • Michelle Kimbara,
    • Pavel Shashkin,
    • Jean F Charlot,
    • Marianna Tcherpakov,
    • Richard Corbett,
    • Angela Tam,
    • Richard Varhol,
    • Duane Smailus,
    • Michelle Moksa,
    • Yongjun Zhao,
    • Allen Delaney,
    • Hong Qian,
    • Inanc Birol,
    • Jacqueline Schein,
    • Richard Moore,
    • Robert Holt,
    • Doug E Horsman,
    • Joseph M Connors,
    • Steven Jones,
    • Samuel Aparicio,
    • Martin Hirst,

    Nature Genetics 42, 181–185 (2010) 10.1038/ng.518

  17. ERG rearrangement is specific to prostate cancer and does not occur in any other common tumor

    • Veit J Scheble,
    • Martin Braun,
    • Rameen Beroukhim,
    • Craig H Mermel,
    • Christian Ruiz,
    • Theresia Wilbertz
    • Ann-Cathrin Stiedl,
    • Karen Petersen,
    • Markus Reischl,
    • Rainer Kuefer,
    • David Schilling,
    • Falko Fend,
    • Glen Kristiansen,
    • Matthew Meyerson,
    • Mark A Rubin,

    Modern Pathology 23, 1061–1067 (2010) 10.1038/modpathol.2010.87

  18. Detailed computational study of p53 and p16: using evolutionary sequence analysis and disease-associated mutations to predict the functional consequences of allelic variants

    • M S Greenblatt,
    • J G Beaudet,
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    • K S Godin,
    • L Trombley,
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    Oncogene 22, 1150–1163 (2003) 10.1038/sj.onc.1206101

  19. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy

    • Jordi Barretina,
    • Barry S Taylor,
    • Shantanu Banerji,
    • Alexis H Ramos,
    • Mariana Lagos-Quintana,
    • Penelope L DeCarolis
    • Kinjal Shah,
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    • Yevgenyi Antipin,
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    • Megan Hanna,
    • Ted Sharpe,
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    • Neerav Shukla,
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    • Serena J Silver,
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    • Wendy Winckler,
    • Robert G Maki,
    • Levi A Garraway,
    • Alex Lash,
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    • William R Sellers,
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    • Eric S Lander,
    • Harold E Varmus,
    • Marc Ladanyi,
    • Chris Sander,

    Nature Genetics 42, 715–721 (2010) 10.1038/ng.619

  20. Not applicable

    Science-Business eXchange 3 (2010) 10.1038/scibx.2010.917

  21. Signatures of mutation and selection in the cancer genome

    • Graham R. Bignell
    • P. Andrew Futreal
    • Michael R. Stratton

    Nature 463, 893–898 (2010) 10.1038/nature08768

  22. 1p36 is a preferential target of chromosome 1 deletions in astrocytic tumours and homozygously deleted in a subset of glioblastomas

    • K Ichimura,
    • A P Vogazianou,
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    • L M Bäcklund,
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    • K Baird,
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    Oncogene 27, 2097–2108 (2007) 10.1038/sj.onc.1210848

  23. Somatic mutations of the Parkinson's disease–associated gene PARK2 in glioblastoma and other human malignancies

    • Selvaraju Veeriah,
    • Barry S Taylor,
    • Shasha Meng,
    • Fang Fang,
    • Emrullah Yilmaz,
    • Igor Vivanco
    • Manickam Janakiraman,
    • Nikolaus Schultz,
    • Aphrothiti J Hanrahan,
    • William Pao,
    • Marc Ladanyi,
    • Chris Sander,
    • Adriana Heguy,
    • Eric C Holland,
    • Philip B Paty,
    • Paul S Mischel,
    • Linda Liau,
    • Timothy F Cloughesy,
    • Ingo K Mellinghoff,

    Nature Genetics 42, 77–82 (2009) 10.1038/ng.491

  24. Mitochondrial mutations in hepatocellular carcinomas and fibrolamellar carcinomas

    • Perumal Vivekanandan,
    • Hubert Daniel,
    • Matthew M Yeh
    • & Michael Torbenson

    Modern Pathology 23, 790–798 (2010) 10.1038/modpathol.2010.51

  25. Genomic profiling of high-risk acute lymphoblastic leukemia

    • J R Collins-Underwood
    • & C G Mullighan

    Leukemia 24, 1676–1685 (2010) 10.1038/leu.2010.177

  26. The Induction of Mutations by a Carcinogen

    • L C Strong

    British Journal of Cancer 3, 97–108 (1949) 10.1038/bjc.1949.12

  27. Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses

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    • R Autio,
    • S Haapa-Paananen,
    • M Wolf,
    • M Saarela,
    • R Grénman
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    Oncogene 25, 6997–7008 (2006) 10.1038/sj.onc.1209690

  28. No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas

    • Wen Qiu,
    • Min Hu,
    • Anita Sridhar,
    • Ken Opeskin,
    • Stephen Fox,
    • Michail Shipitsin
    • Melanie Trivett,
    • Ella R Thompson,
    • Manasa Ramakrishna,
    • Kylie L Gorringe,
    • Kornelia Polyak,

    Nature Genetics 40, 650–655 (2008) 10.1038/ng.117

  29. Disruption of Brca2 increases the spontaneous mutation rate in vivo: synergism with ionizing radiation

    • Andrew N.J. Tutt,
    • Conny Th.M. van Oostrom,
    • Gillian M. Ross,
    • Harry van Steeg
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    EMBO reports 3, 255–260 (2002) 10.1093/embo-reports/kvf037

  30. International network of cancer genome projects

    Nature 464, 993–998 (2010) 10.1038/nature08987

  31. Characterization of candidate gene copy number alterations in the 11q13 region along with BRAF and NRAS mutations in human melanoma

    • Viktória Lázár
    • Szilvia Ecsedi
    • Attila G Szöllősi
    • Réka Tóth
    • Laura Vízkeleti
    • Zsuzsa Rákosy
    • Ágnes Bégány
    • Róza Ádány
    • Margit Balázs

    Modern Pathology 22, 1367–1378 (2009) 10.1038/modpathol.2009.109

  32. DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway

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    • H Yamashita,
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    • A N Miller,
    • A L Gonzalez,
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    • A Jiang,
    • Y Yi,
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    Oncogene 29, 6331–6342 (2010) 10.1038/onc.2010.362

  33. Antibody diversification by somatic mutation: from Burnet onwards

    • Michael S Neuberger

    Immunology and Cell Biology 86, 124–132 (2008) 10.1038/sj.icb.7100160

  34. The pattern of natural selection in somatic cancer mutations of human mtDNA

    • Pete Stafford
    • & Estella B Chen-Quin

    Journal of Human Genetics 55, 605–612 (2010) 10.1038/jhg.2010.76

  35. Mutation of the PIK3CA oncogene in human cancers

    • B Karakas,
    • K E Bachman
    • & B H Park

    British Journal of Cancer 94, 455–459 (2006) 10.1038/sj.bjc.6602970

  36. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

    • Sohrab P. Shah,
    • Ryan D. Morin,
    • Jaswinder Khattra,
    • Leah Prentice,
    • Trevor Pugh,
    • Angela Burleigh
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    • Karen Gelmon,
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    • Janine Senz,
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    • Robert A. Holt,
    • Steven Jones,
    • Mark Sun,
    • Gillian Leung,
    • Richard Moore,
    • Tesa Severson,
    • Greg A. Taylor,
    • Andrew E. Teschendorff,
    • Kane Tse,
    • Gulisa Turashvili,
    • Richard Varhol,
    • René L. Warren,
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    • Yongjun Zhao,
    • Carlos Caldas,
    • David Huntsman,
    • Martin Hirst,

    Nature 461, 809–813 (2009) 10.1038/nature08489

  37. Somatic EGFR mutations and efficacy of tyrosine kinase inhibitors in NSCLC

    • Helena Linardou,
    • Issa J. Dahabreh,
    • Dimitrios Bafaloukos,
    • Paris Kosmidis
    • & Samuel Murray

    Nature Reviews Clinical Oncology 6, 352–366 (2009) 10.1038/nrclinonc.2009.62

  38. Refining the relation between ‘first hits’ and ‘second hits’ at the APC locus: the ‘loose fit’ model and evidence for differences in somatic mutation spectra among patients

    • Michael Crabtree,
    • Oliver M Sieber,
    • Lara Lipton,
    • Shirley V Hodgson,
    • Hanan Lamlum,
    • Hunu J W Thomas
    • Kay Neale,
    • Robin K S Phillips,

    Oncogene 22, 4257–4265 (2003) 10.1038/sj.onc.1206471

  39. From cancer genomes to cancer models: bridging the gaps

    • Anaïs Baudot,
    • Francisco X. Real,
    • José M. G. Izarzugaza
    • & Alfonso Valencia

    EMBO reports 10, 359–366 (2009) 10.1038/embor.2009.46

  40. BCR–ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros

    • Charles G. Mullighan,
    • Christopher B. Miller,
    • Ina Radtke,
    • Letha A. Phillips,
    • James Dalton,
    • Jing Ma
    • Deborah White,
    • Timothy P. Hughes,
    • Michelle M. Le Beau,
    • Ching-Hon Pui,
    • Mary V. Relling,

    Nature 453, 110–114 (2008) 10.1038/nature06866

  41. Mitochondrial mutations in cancer

    • M Brandon
    • P Baldi
    • D C Wallace

    Oncogene 25, 4647–4662 (2006) 10.1038/sj.onc.1209607

  42. Molecular and cellular aspects of HTLV-1 associated leukemogenesis in vivo

    • F Mortreux,
    • A-S Gabet
    • & E Wattel

    Leukemia 17, 26–38 (2002) 10.1038/sj.leu.2402777

  43. The landscape of somatic copy-number alteration across human cancers

    • Rameen Beroukhim,
    • Craig H. Mermel,
    • Dale Porter,
    • Guo Wei,
    • Soumya Raychaudhuri,
    • Jerry Donovan
    • Jordi Barretina,
    • Jesse S. Boehm,
    • Jennifer Dobson,
    • Mitsuyoshi Urashima,
    • Kevin T. Mc Henry,
    • Reid M. Pinchback,
    • Azra H. Ligon,
    • Yoon-Jae Cho,
    • Leila Haery,
    • Heidi Greulich,
    • Michael Reich,
    • Wendy Winckler,
    • Michael S. Lawrence,
    • Barbara A. Weir,
    • Kumiko E. Tanaka,
    • Derek Y. Chiang,
    • Adam J. Bass,
    • Alice Loo,
    • Carter Hoffman,
    • John Prensner,
    • Ted Liefeld,
    • Qing Gao,
    • Derek Yecies,
    • Sabina Signoretti,
    • Elizabeth Maher,
    • Frederic J. Kaye,
    • Hidefumi Sasaki,
    • Joel E. Tepper,
    • Jonathan A. Fletcher,
    • Josep Tabernero,
    • José Baselga,
    • Ming-Sound Tsao,
    • Francesca Demichelis,
    • Mark A. Rubin,
    • Pasi A. Janne,
    • Mark J. Daly,
    • Carmelo Nucera,
    • Ross L. Levine,
    • Benjamin L. Ebert,
    • Stacey Gabriel,
    • Anil K. Rustgi,
    • Cristina R. Antonescu,
    • Marc Ladanyi,
    • Anthony Letai,
    • Levi A. Garraway,
    • Massimo Loda,
    • David G. Beer,
    • Lawrence D. True,
    • Aikou Okamoto,
    • Scott L. Pomeroy,
    • Samuel Singer,
    • Todd R. Golub,
    • Eric S. Lander,
    • Gad Getz,

    Nature 463, 899–905 (2010) 10.1038/nature08822

  44. The molecular pathology of cancer

    • Timothy J. R. Harris
    • & Frank McCormick

    Nature Reviews Clinical Oncology 7, 251–265 (2010) 10.1038/nrclinonc.2010.41

  45. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

    • Timothy J. Ley,
    • Elaine R. Mardis,
    • Li Ding,
    • Bob Fulton,
    • Michael D. McLellan,
    • Ken Chen
    • David Dooling,
    • Brian H. Dunford-Shore,
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    • Lisa Cook,
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    • David E. Larson,
    • Dan C. Koboldt,
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    • Amy Hawkins,
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    • Tracie Miner,
    • Lucinda Fulton,
    • Vincent Magrini,
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    • Jarret Glasscock,
    • Joshua Conyers,
    • Nathan Sander,
    • Xiaoqi Shi,
    • John R. Osborne,
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    • David Gordon,
    • Asif Chinwalla,
    • Yu Zhao,
    • Rhonda E. Ries,
    • Jacqueline E. Payton,
    • Peter Westervelt,
    • Michael H. Tomasson,
    • Mark Watson,
    • Jack Baty,
    • Jennifer Ivanovich,
    • Sharon Heath,
    • William D. Shannon,
    • Rakesh Nagarajan,
    • Matthew J. Walter,
    • Daniel C. Link,
    • Timothy A. Graubert,

    Nature 456, 66–72 (2008) 10.1038/nature07485

  46. Highly efficient somatic-mutation identification using Escherichia coli mismatch-repair detection

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    Nature Methods 4, 713–715 (2007) 10.1038/nmeth1081

  47. Somatic Mutation Analysis in Tumor Samples using the Sequenom MassARRAY® System

    • Marisa Pearce
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    (2010) 10.1038/an7545

  48. A comparison of the instabilities at the Nivea and Pallida loci in Antirrhinum majus

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  49. Somatic mutation hotspots correlate with DNA polymerase η error spectrum

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    Nature Immunology 2, 530–536 (2001) 10.1038/88732

  50. Molecular alterations of EGFR and PTEN in prostate cancer: association with high-grade and advanced-stage carcinomas

    • Silvia de Muga,
    • Silvia Hernández,
    • Laia Agell,
    • Marta Salido,
    • Nuria Juanpere,
    • Marta Lorenzo
    • José A Lorente,

    Modern Pathology 23, 703–712 (2010) 10.1038/modpathol.2010.45

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