Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
Tatiana Popova,Elodie Manié,Dominique Stoppa-Lyonnet,Guillem Rigaill,Guillem Rigaill,Emmanuel Barillot,Emmanuel Barillot,Marc-Henri Stern +7 more
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TLDR
This work describes a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles.Abstract:
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.read more
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Whole genomes redefine the mutational landscape of pancreatic cancer.
Nicola Waddell,Marina Pajic,Ann-Marie Patch,David K. Chang,Karin S. Kassahn,Peter Bailey,Amber L. Johns,David Miller,Katia Nones,Kelly Quek,Michael C.J. Quinn,Alan J. Robertson,Muhammad Zaki Hidayatullah Fadlullah,Timothy J. C. Bruxner,Angelika N. Christ,Ivon Harliwong,Senel Idrisoglu,Suzanne Manning,Craig Nourse,Ehsan Nourbakhsh,Shivangi Wani,Peter J. Wilson,Emma Markham,Nicole Cloonan,Matthew J. Anderson,J. Lynn Fink,Oliver Holmes,Stephen H. Kazakoff,Conrad Leonard,Felicity Newell,Barsha Poudel,Sarah Song,Darrin Taylor,Nick Waddell,Scott Wood,Qinying Xu,Jianmin Wu,Mark Pinese,Mark J. Cowley,Hong C. Lee,Marc D. Jones,Adnan Nagrial,Jeremy L. Humphris,Lorraine A. Chantrill,Venessa T. Chin,Angela Steinmann,Amanda Mawson,Emily S. Humphrey,Emily K. Colvin,Angela Chou,Christopher J. Scarlett,Andreia V. Pinho,Marc Giry-Laterriere,Ilse Rooman,Jaswinder S. Samra,James G. Kench,Jessica A. Pettitt,Neil D. Merrett,Christopher W. Toon,Krishna Epari,Nam Q. Nguyen,Andrew Barbour,Nikolajs Zeps,Nigel B. Jamieson,Janet Graham,Simone P. Niclou,Rolf Bjerkvig,Robert Grützmann,Daniela Aust,Ralph H. Hruban,Anirban Maitra,Christine A. Iacobuzio-Donahue,Christopher L. Wolfgang,Richard A. Morgan,Rita T. Lawlor,Vincenzo Corbo,Claudio Bassi,Massimo Falconi,Giuseppe Zamboni,Giampaolo Tortora,Margaret A. Tempero,Anthony J. Gill,James R. Eshleman,Christian Pilarsky,Aldo Scarpa,Elizabeth A. Musgrove,John V. Pearson,Andrew V. Biankin,Sean M. Grimmond +88 more
TL;DR: Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency, and 4 of 5 individuals with these measures of defective DNA maintenance responded to platinum therapy.
Journal ArticleDOI
Absolute quantification of somatic DNA alterations in human cancer
Scott L. Carter,Kristian Cibulskis,Elena Helman,Elena Helman,Aaron McKenna,Hui Shen,Travis I. Zack,Peter W. Laird,Robert C. Onofrio,Wendy Winckler,Barbara A. Weir,Rameen Beroukhim,Rameen Beroukhim,Rameen Beroukhim,David Pellman,Douglas A. Levine,Eric S. Lander,Eric S. Lander,Eric S. Lander,Matthew Meyerson,Matthew Meyerson,Gad Getz +21 more
TL;DR: A computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations is described, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression.
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
TL;DR: It is shown that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance.
Journal ArticleDOI
Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma
Cécile Guichard,Giuliana Amaddeo,Giuliana Amaddeo,Sandrine Imbeaud,Sandrine Imbeaud,Yannick Ladeiro,Yannick Ladeiro,Laura Pelletier,Laura Pelletier,Ichrafe Ben Maad,Ichrafe Ben Maad,Julien Calderaro,Julien Calderaro,Paulette Bioulac-Sage,Mélanie Letexier,Françoise Degos,Bruno Clément,Charles Balabaud,Eric Chevet,Alexis Laurent,Gabrielle Couchy,Gabrielle Couchy,Eric Letouzé,Fabien Calvo,Jessica Zucman-Rossi,Jessica Zucman-Rossi +25 more
TL;DR: Functional analyses showed tumor suppressor properties for IRF2, whose inactivation, exclusively found in hepatitis B virus-related tumors, led to impaired TP53 function, and association of mutations in specific genes suggested that Wnt/β-catenin signaling might cooperate in liver carcinogenesis with both oxidative stress metabolism and Ras/mitogen-activated protein kinase (MAPK) pathways.
Journal ArticleDOI
Control-FREEC
Valentina Boeva,Tatiana Popova,Kevin Bleakley,Pierre Chiche,Julie Cappo,Gudrun Schleiermacher,Isabelle Janoueix-Lerosey,Olivier Delattre,Emmanuel Barillot +8 more
TL;DR: The tool Control-FREEC is presented, that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH.
References
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