Journal ArticleDOI
Whole-genome characterization of chemoresistant ovarian cancer
Ann-Marie Patch,Ann-Marie Patch,Elizabeth L. Christie,Dariush Etemadmoghadam,Dariush Etemadmoghadam,Dale W. Garsed,Joshy George,Sian Fereday,Katia Nones,Katia Nones,Prue A. Cowin,Kathryn Alsop,Peter Bailey,Peter Bailey,Karin S. Kassahn,Karin S. Kassahn,Felicity Newell,Michael C.J. Quinn,Michael C.J. Quinn,Stephen H. Kazakoff,Stephen H. Kazakoff,Kelly Quek,Charlotte Wilhelm-Benartzi,Edward Curry,Huei San Leong,Anne Hamilton,Anne Hamilton,Anne Hamilton,Linda Mileshkin,George Au-Yeung,Catherine Kennedy,Jillian Hung,Yoke Eng Chiew,Paul R. Harnett,Michael Friedlander,Michael C. J. Quinn,Jan Pyman,Stephen Cordner,Patricia C. M. O’Brien,Jodie Leditschke,Greg Young,Kate Strachan,Paul Waring,Walid J Azar,Chris Mitchell,Nadia Traficante,Joy Hendley,Heather Thorne,Mark Shackleton,David Miller,Gisela Mir Arnau,Richard W. Tothill,Timothy P. Holloway,Timothy Semple,Ivon Harliwong,Craig Nourse,Ehsan Nourbakhsh,Suzanne Manning,Senel Idrisoglu,Timothy J. C. Bruxner,Angelika N. Christ,Barsha Poudel,Oliver Holmes,Oliver Holmes,Matthew J. Anderson,Conrad Leonard,Conrad Leonard,Andrew Lonie,Nathan E. Hall,Scott Wood,Scott Wood,Darrin Taylor,Qinying Xu,Qinying Xu,J. Lynn Fink,Nick Waddell,Ronny Drapkin,Euan A. Stronach,Hani Gabra,Robert S. Brown,A. Jewell,Shivashankar H. Nagaraj,Emma Markham,Peter Wilson,Jason Ellul,Orla McNally,Maria A. Doyle,Ravikiran Vedururu,Collin Stewart,Ernst Lengyel,John V. Pearson,John V. Pearson,Nicola Waddell,Nicola Waddell,Anna deFazio,Sean M. Grimmond,Sean M. Grimmond,David D.L. Bowtell,David D.L. Bowtell,David D.L. Bowtell +99 more
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It is shown that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance.Abstract:
Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.read more
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Journal ArticleDOI
Genomic analyses identify molecular subtypes of pancreatic cancer
Peter Bailey,David K. Chang,Katia Nones,Katia Nones,Amber L. Johns,Ann-Marie Patch,Ann-Marie Patch,Marie-Claude Gingras,David Miller,David Miller,Angelika N. Christ,Timothy J. C. Bruxner,Michael C.J. Quinn,Michael C.J. Quinn,Craig Nourse,Craig Nourse,Murtaugh Lc,Ivon Harliwong,Senel Idrisoglu,Suzanne Manning,Ehsan Nourbakhsh,Shivangi Wani,Shivangi Wani,J. Lynn Fink,Oliver Holmes,Oliver Holmes,Chin,Matthew J. Anderson,Stephen H. Kazakoff,Stephen H. Kazakoff,Conrad Leonard,Conrad Leonard,Felicity Newell,Nicola Waddell,Scott Wood,Scott Wood,Qinying Xu,Qinying Xu,Peter J. Wilson,Nicole Cloonan,Nicole Cloonan,Karin S. Kassahn,Karin S. Kassahn,Karin S. Kassahn,Darrin Taylor,Kelly Quek,Alan J. Robertson,Lorena Pantano,Laura Mincarelli,Luis Navarro Sanchez,Lisa Evers,Jianmin Wu,Mark Pinese,Mark J. Cowley,Jones,Jones,Emily K. Colvin,Adnan Nagrial,Emily S. Humphrey,Lorraine A. Chantrill,Lorraine A. Chantrill,Amanda Mawson,Jeremy L. Humphris,Angela Chou,Angela Chou,Marina Pajic,Marina Pajic,Christopher J. Scarlett,Christopher J. Scarlett,Andreia V. Pinho,Marc Giry-Laterriere,Ilse Rooman,Jaswinder S. Samra,James G. Kench,James G. Kench,James G. Kench,Jessica A. Lovell,Neil D. Merrett,Christopher W. Toon,Krishna Epari,Nam Q. Nguyen,Andrew Barbour,Nikolajs Zeps,Kim Moran-Jones,Nigel B. Jamieson,Janet Graham,Janet Graham,Fraser Duthie,Karin A. Oien,Karin A. Oien,Hair J,Robert Grützmann,Anirban Maitra,Christine A. Iacobuzio-Donahue,Christopher L. Wolfgang,Richard A. Morgan,Rita T. Lawlor,Corbo,Claudio Bassi,Borislav Rusev,Paola Capelli,Roberto Salvia,Giampaolo Tortora,Debabrata Mukhopadhyay,Gloria M. Petersen,Munzy Dm,William E. Fisher,Saadia A. Karim,Eshleman,Ralph H. Hruban,Christian Pilarsky,Jennifer P. Morton,Owen J. Sansom,Aldo Scarpa,Elizabeth A. Musgrove,Ulla-Maja Bailey,Oliver Hofmann,Oliver Hofmann,R. L. Sutherland,David A. Wheeler,Anthony J. Gill,Anthony J. Gill,Richard A. Gibbs,John V. Pearson,John V. Pearson,Andrew V. Biankin,Sean M. Grimmond,Sean M. Grimmond,Sean M. Grimmond +128 more
TL;DR: Detailed genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing.
Integrative Genomics Viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Journal ArticleDOI
A view on drug resistance in cancer
TL;DR: A reductionist approach is taken to define and separate the key determinants of drug resistance, which include tumour burden and growth kinetics; tumour heterogeneity; physical barriers; the immune system and the microenvironment; undruggable cancer drivers; and the many consequences of applying therapeutic pressures.
Journal ArticleDOI
Revisiting the role of ABC transporters in multidrug-resistant cancer
Robert W. Robey,Kristen M. Pluchino,Matthew D. Hall,Antonio Tito Fojo,Antonio Tito Fojo,Susan E. Bates,Susan E. Bates,Michael M. Gottesman +7 more
TL;DR: Evidence is presented indicating that it is time to revisit the investigation into the role of ABC transporters in efficient drug delivery in various cancer types and at the blood–brain barrier, and push forward their clinical application as biomarkers and as targets in combination therapies in order to improve anticancer drug efficiency.
Journal ArticleDOI
Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1): an international, multicentre, open-label, phase 2 trial
Elizabeth M. Swisher,Kevin K. Lin,Amit M. Oza,Clare L. Scott,Heidi Giordano,James Sun,Gottfried E. Konecny,Robert L. Coleman,Anna V. Tinker,David M. O'Malley,Rebecca Kristeleit,Ling Ma,Katherine M. Bell-McGuinn,James D. Brenton,Janiel M. Cragun,Ana Oaknin,Isabelle Ray-Coquard,Maria I. Harrell,Elaina Mann,Scott H. Kaufmann,Anne Floquet,Alexandra Leary,Thomas Harding,Sandra Goble,Lara Maloney,Jeff Isaacson,Andrew R. Allen,Lindsey Rolfe,Roman Yelensky,Mitch Raponi,Iain A. McNeish +30 more
TL;DR: The ability of tumour genomic LOH, quantified with a next-generation sequencing assay, to predict response to rucaparib, an oral PARP inhibitor, was assessed in ARIEL2, an international, multicentre, two-part, phase 2, open-label study.
References
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Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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Integrative genomics viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: In this article, the authors present an approach for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
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