Literature DB >> 24675517

Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Paul C Boutros1,2,3, Adam A Margolin4, Joshua M Stuart5, Adam D Ewing5, Kyle Ellrott5, Thea C Norman4, Kristen K Dang4, Yin Hu4, Michael R Kellen4, Christine Suver4, J Christopher Bare4, Lincoln D Stein1,6, Paul T Spellman7, Gustavo Stolovitzky8, Stephen H Friend4.   

Abstract

Entities:  

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Year:  2014        PMID: 24675517      PMCID: PMC4035501          DOI: 10.1038/ng.2932

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


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  10 in total

1.  The Cancer Genome Atlas Pan-Cancer analysis project.

Authors:  John N Weinstein; Eric A Collisson; Gordon B Mills; Kenna R Mills Shaw; Brad A Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M Stuart
Journal:  Nat Genet       Date:  2013-10       Impact factor: 38.330

2.  Towards a rigorous assessment of systems biology models: the DREAM3 challenges.

Authors:  Robert J Prill; Daniel Marbach; Julio Saez-Rodriguez; Peter K Sorger; Leonidas G Alexopoulos; Xiaowei Xue; Neil D Clarke; Gregoire Altan-Bonnet; Gustavo Stolovitzky
Journal:  PLoS One       Date:  2010-02-23       Impact factor: 3.240

3.  Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.

Authors:  Adam A Margolin; Erhan Bilal; Erich Huang; Thea C Norman; Lars Ottestad; Brigham H Mecham; Ben Sauerwine; Michael R Kellen; Lara M Mangravite; Matthew D Furia; Hans Kristian Moen Vollan; Oscar M Rueda; Justin Guinney; Nicole A Deflaux; Bruce Hoff; Xavier Schildwachter; Hege G Russnes; Daehoon Park; Veronica O Vang; Tyler Pirtle; Lamia Youseff; Craig Citro; Christina Curtis; Vessela N Kristensen; Joseph Hellerstein; Stephen H Friend; Gustavo Stolovitzky; Samuel Aparicio; Carlos Caldas; Anne-Lise Børresen-Dale
Journal:  Sci Transl Med       Date:  2013-04-17       Impact factor: 17.956

4.  Taking pan-cancer analysis global.

Authors: 
Journal:  Nat Genet       Date:  2013-11       Impact factor: 38.330

Review 5.  Genome structural variation discovery and genotyping.

Authors:  Can Alkan; Bradley P Coe; Evan E Eichler
Journal:  Nat Rev Genet       Date:  2011-03-01       Impact factor: 53.242

6.  Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.

Authors:  Li Ding; Timothy J Ley; David E Larson; Christopher A Miller; Daniel C Koboldt; John S Welch; Julie K Ritchey; Margaret A Young; Tamara Lamprecht; Michael D McLellan; Joshua F McMichael; John W Wallis; Charles Lu; Dong Shen; Christopher C Harris; David J Dooling; Robert S Fulton; Lucinda L Fulton; Ken Chen; Heather Schmidt; Joelle Kalicki-Veizer; Vincent J Magrini; Lisa Cook; Sean D McGrath; Tammi L Vickery; Michael C Wendl; Sharon Heath; Mark A Watson; Daniel C Link; Michael H Tomasson; William D Shannon; Jacqueline E Payton; Shashikant Kulkarni; Peter Westervelt; Matthew J Walter; Timothy A Graubert; Elaine R Mardis; Richard K Wilson; John F DiPersio
Journal:  Nature       Date:  2012-01-11       Impact factor: 49.962

7.  Signatures of mutational processes in human cancer.

Authors:  Ludmil B Alexandrov; Serena Nik-Zainal; David C Wedge; Samuel A J R Aparicio; Sam Behjati; Andrew V Biankin; Graham R Bignell; Niccolò Bolli; Ake Borg; Anne-Lise Børresen-Dale; Sandrine Boyault; Birgit Burkhardt; Adam P Butler; Carlos Caldas; Helen R Davies; Christine Desmedt; Roland Eils; Jórunn Erla Eyfjörd; John A Foekens; Mel Greaves; Fumie Hosoda; Barbara Hutter; Tomislav Ilicic; Sandrine Imbeaud; Marcin Imielinski; Marcin Imielinsk; Natalie Jäger; David T W Jones; David Jones; Stian Knappskog; Marcel Kool; Sunil R Lakhani; Carlos López-Otín; Sancha Martin; Nikhil C Munshi; Hiromi Nakamura; Paul A Northcott; Marina Pajic; Elli Papaemmanuil; Angelo Paradiso; John V Pearson; Xose S Puente; Keiran Raine; Manasa Ramakrishna; Andrea L Richardson; Julia Richter; Philip Rosenstiel; Matthias Schlesner; Ton N Schumacher; Paul N Span; Jon W Teague; Yasushi Totoki; Andrew N J Tutt; Rafael Valdés-Mas; Marit M van Buuren; Laura van 't Veer; Anne Vincent-Salomon; Nicola Waddell; Lucy R Yates; Jessica Zucman-Rossi; P Andrew Futreal; Ultan McDermott; Peter Lichter; Matthew Meyerson; Sean M Grimmond; Reiner Siebert; Elías Campo; Tatsuhiro Shibata; Stefan M Pfister; Peter J Campbell; Michael R Stratton
Journal:  Nature       Date:  2013-08-14       Impact factor: 49.962

8.  Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

Authors:  Jason O'Rawe; Tao Jiang; Guangqing Sun; Yiyang Wu; Wei Wang; Jingchu Hu; Paul Bodily; Lifeng Tian; Hakon Hakonarson; W Evan Johnson; Zhi Wei; Kai Wang; Gholson J Lyon
Journal:  Genome Med       Date:  2013-03-27       Impact factor: 11.117

9.  Comparing somatic mutation-callers: beyond Venn diagrams.

Authors:  Su Yeon Kim; Terence P Speed
Journal:  BMC Bioinformatics       Date:  2013-06-10       Impact factor: 3.169

10.  Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Authors:  Michael S Lawrence; Petar Stojanov; Paz Polak; Gregory V Kryukov; Kristian Cibulskis; Andrey Sivachenko; Scott L Carter; Chip Stewart; Craig H Mermel; Steven A Roberts; Adam Kiezun; Peter S Hammerman; Aaron McKenna; Yotam Drier; Lihua Zou; Alex H Ramos; Trevor J Pugh; Nicolas Stransky; Elena Helman; Jaegil Kim; Carrie Sougnez; Lauren Ambrogio; Elizabeth Nickerson; Erica Shefler; Maria L Cortés; Daniel Auclair; Gordon Saksena; Douglas Voet; Michael Noble; Daniel DiCara; Pei Lin; Lee Lichtenstein; David I Heiman; Timothy Fennell; Marcin Imielinski; Bryan Hernandez; Eran Hodis; Sylvan Baca; Austin M Dulak; Jens Lohr; Dan-Avi Landau; Catherine J Wu; Jorge Melendez-Zajgla; Alfredo Hidalgo-Miranda; Amnon Koren; Steven A McCarroll; Jaume Mora; Brian Crompton; Robert Onofrio; Melissa Parkin; Wendy Winckler; Kristin Ardlie; Stacey B Gabriel; Charles W M Roberts; Jaclyn A Biegel; Kimberly Stegmaier; Adam J Bass; Levi A Garraway; Matthew Meyerson; Todd R Golub; Dmitry A Gordenin; Shamil Sunyaev; Eric S Lander; Gad Getz
Journal:  Nature       Date:  2013-06-16       Impact factor: 49.962

  10 in total
  28 in total

1.  DREAMing of benchmarks.

Authors:  Irene Jarchum; Susan Jones
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

Review 2.  Cancer whole-genome sequencing: present and future.

Authors:  H Nakagawa; C P Wardell; M Furuta; H Taniguchi; A Fujimoto
Journal:  Oncogene       Date:  2015-03-30       Impact factor: 9.867

Review 3.  Crowdsourcing biomedical research: leveraging communities as innovation engines.

Authors:  Julio Saez-Rodriguez; James C Costello; Stephen H Friend; Michael R Kellen; Lara Mangravite; Pablo Meyer; Thea Norman; Gustavo Stolovitzky
Journal:  Nat Rev Genet       Date:  2016-07-15       Impact factor: 53.242

Review 4.  Approaches to integrating germline and tumor genomic data in cancer research.

Authors:  Heather Spencer Feigelson; Katrina A B Goddard; Celine Hollombe; Sharna R Tingle; Elizabeth M Gillanders; Leah E Mechanic; Stefanie A Nelson
Journal:  Carcinogenesis       Date:  2014-08-12       Impact factor: 4.944

5.  Onco-proteogenomics: cancer proteomics joins forces with genomics.

Authors:  Javier A Alfaro; Ankit Sinha; Thomas Kislinger; Paul C Boutros
Journal:  Nat Methods       Date:  2014-11       Impact factor: 28.547

Review 6.  The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations.

Authors:  Margherita Bodini; Chiara Ronchini; Luciano Giacò; Anna Russo; Giorgio E M Melloni; Lucilla Luzi; Domenico Sardella; Sara Volorio; Syed K Hasan; Tiziana Ottone; Serena Lavorgna; Francesco Lo-Coco; Anna Candoni; Renato Fanin; Eleonora Toffoletti; Ilaria Iacobucci; Giovanni Martinelli; Alessandro Cignetti; Corrado Tarella; Loris Bernard; Pier Giuseppe Pelicci; Laura Riva
Journal:  Blood       Date:  2014-12-12       Impact factor: 22.113

7.  Optimizing cancer genome sequencing and analysis.

Authors:  Malachi Griffith; Christopher A Miller; Obi L Griffith; Kilannin Krysiak; Zachary L Skidmore; Avinash Ramu; Jason R Walker; Ha X Dang; Lee Trani; David E Larson; Ryan T Demeter; Michael C Wendl; Joshua F McMichael; Rachel E Austin; Vincent Magrini; Sean D McGrath; Amy Ly; Shashikant Kulkarni; Matthew G Cordes; Catrina C Fronick; Robert S Fulton; Christopher A Maher; Li Ding; Jeffery M Klco; Elaine R Mardis; Timothy J Ley; Richard K Wilson
Journal:  Cell Syst       Date:  2015-09-23       Impact factor: 10.304

8.  Toward better benchmarking: challenge-based methods assessment in cancer genomics.

Authors:  Paul C Boutros; Adam A Margolin; Joshua M Stuart; Andrea Califano; Gustavo Stolovitzky
Journal:  Genome Biol       Date:  2014-09-17       Impact factor: 13.583

Review 9.  The path to routine use of genomic biomarkers in the cancer clinic.

Authors:  Paul C Boutros
Journal:  Genome Res       Date:  2015-10       Impact factor: 9.043

10.  Facilitating a culture of responsible and effective sharing of cancer genome data.

Authors:  Lillian L Siu; Mark Lawler; David Haussler; Bartha Maria Knoppers; Jeremy Lewin; Daniel J Vis; Rachel G Liao; Fabrice Andre; Ian Banks; J Carl Barrett; Carlos Caldas; Anamaria Aranha Camargo; Rebecca C Fitzgerald; Mao Mao; John E Mattison; William Pao; William R Sellers; Patrick Sullivan; Bin Tean Teh; Robyn L Ward; Jean Claude ZenKlusen; Charles L Sawyers; Emile E Voest
Journal:  Nat Med       Date:  2016-05-05       Impact factor: 53.440

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