Literature DB >> 25157968

Prospective enterprise-level molecular genotyping of a cohort of cancer patients.

Laura E MacConaill1, Elizabeth Garcia2, Priyanka Shivdasani2, Matthew Ducar3, Ravali Adusumilli3, Marc Breneiser3, Mark Byrne2, Lawrence Chung2, Jodie Conneely2, Lauren Crosby2, Levi A Garraway4, Xin Gong2, William C Hahn4, Charlie Hatton3, Philip W Kantoff5, Michael Kluk2, Frank Kuo2, Yonghui Jia2, Ruchi Joshi2, Janina Longtine2, Allison Manning2, Emanuele Palescandolo3, Nematullah Sharaf2, Lynette Sholl2, Paul van Hummelen3, Jacqueline Wade2, Bruce M Wollinson3, Dimity Zepf2, Barrett J Rollins5, Neal I Lindeman6.   

Abstract

Ongoing cancer genome characterization studies continue to elucidate the spectrum of genomic abnormalities that drive many cancers, and in the clinical arena assessment of the driver genetic alterations in patients is playing an increasingly important diagnostic and/or prognostic role for many cancer types. However, the landscape of genomic abnormalities is still unknown for less common cancers, and the influence of specific genotypes on clinical behavior is often still unclear. To address some of these deficiencies, we developed Profile, a prospective cohort study to obtain genomic information on all patients at a large tertiary care medical center for cancer-related care. We enrolled patients with any cancer diagnosis, and, for each patient (unselected for cancer site or type) we applied mass spectrometric genotyping (OncoMap) of 471 common recurrent mutations in 41 cancer-related genes. We report the results of the first 5000 patients, of which 26% exhibited potentially actionable somatic mutations. These observations indicate the utility of genotyping in advancing the field of precision oncology.
Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

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Year:  2014        PMID: 25157968      PMCID: PMC4210463          DOI: 10.1016/j.jmoldx.2014.06.004

Source DB:  PubMed          Journal:  J Mol Diagn        ISSN: 1525-1578            Impact factor:   5.568


  59 in total

1.  Improved survival with vemurafenib in melanoma with BRAF V600E mutation.

Authors:  Paul B Chapman; Axel Hauschild; Caroline Robert; John B Haanen; Paolo Ascierto; James Larkin; Reinhard Dummer; Claus Garbe; Alessandro Testori; Michele Maio; David Hogg; Paul Lorigan; Celeste Lebbe; Thomas Jouary; Dirk Schadendorf; Antoni Ribas; Steven J O'Day; Jeffrey A Sosman; John M Kirkwood; Alexander M M Eggermont; Brigitte Dreno; Keith Nolop; Jiang Li; Betty Nelson; Jeannie Hou; Richard J Lee; Keith T Flaherty; Grant A McArthur
Journal:  N Engl J Med       Date:  2011-06-05       Impact factor: 91.245

2.  Multiplex mutation screening by mass spectrometry evaluation of 820 cases from a personalized cancer medicine registry.

Authors:  Carol Beadling; Michael C Heinrich; Andrea Warrick; Erin M Forbes; Dylan Nelson; Emily Justusson; Judith Levine; Tanaya L Neff; Janice Patterson; Ajia Presnell; Arin McKinley; Laura J Winter; Christie Dewey; Amy Harlow; Oscar Barney; Brian J Druker; Kathryn G Schuff; Christopher L Corless
Journal:  J Mol Diagn       Date:  2011-07-02       Impact factor: 5.568

3.  BRAF mutations in hairy-cell leukemia.

Authors:  Enrico Tiacci; Vladimir Trifonov; Gianluca Schiavoni; Antony Holmes; Wolfgang Kern; Maria Paola Martelli; Alessandra Pucciarini; Barbara Bigerna; Roberta Pacini; Victoria A Wells; Paolo Sportoletti; Valentina Pettirossi; Roberta Mannucci; Oliver Elliott; Arcangelo Liso; Achille Ambrosetti; Alessandro Pulsoni; Francesco Forconi; Livio Trentin; Gianpietro Semenzato; Giorgio Inghirami; Monia Capponi; Francesco Di Raimondo; Caterina Patti; Luca Arcaini; Pellegrino Musto; Stefano Pileri; Claudia Haferlach; Susanne Schnittger; Giovanni Pizzolo; Robin Foà; Laurent Farinelli; Torsten Haferlach; Laura Pasqualucci; Raul Rabadan; Brunangelo Falini
Journal:  N Engl J Med       Date:  2011-06-11       Impact factor: 91.245

4.  Randomized phase II study of erlotinib plus tivantinib versus erlotinib plus placebo in previously treated non-small-cell lung cancer.

Authors:  Lecia V Sequist; Joachim von Pawel; Edward G Garmey; Wallace L Akerley; Wolfram Brugger; Dora Ferrari; Yinpu Chen; Daniel B Costa; David E Gerber; Sergey Orlov; Rodryg Ramlau; Susan Arthur; Igor Gorbachevsky; Brian Schwartz; Joan H Schiller
Journal:  J Clin Oncol       Date:  2011-07-18       Impact factor: 44.544

5.  Tumor epidermal growth factor receptor genotype and depression in stage IV non-small cell lung cancer.

Authors:  William F Pirl; Lara Traeger; Joseph A Greer; Heather Bemis; Emily Gallagher; Inga Lennes; Lecia Sequist; Rebecca Heist; Jennifer S Temel
Journal:  Oncologist       Date:  2011-08-01

6.  Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.

Authors:  Sergey I Nikolaev; Donata Rimoldi; Christian Iseli; Armand Valsesia; Daniel Robyr; Corinne Gehrig; Keith Harshman; Michel Guipponi; Olesya Bukach; Vincent Zoete; Olivier Michielin; Katja Muehlethaler; Daniel Speiser; Jacques S Beckmann; Ioannis Xenarios; Thanos D Halazonetis; C Victor Jongeneel; Brian J Stevenson; Stylianos E Antonarakis
Journal:  Nat Genet       Date:  2011-12-25       Impact factor: 38.330

7.  Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors.

Authors:  Lecia V Sequist; Belinda A Waltman; Dora Dias-Santagata; Subba Digumarthy; Alexa B Turke; Panos Fidias; Kristin Bergethon; Alice T Shaw; Scott Gettinger; Arjola K Cosper; Sara Akhavanfard; Rebecca S Heist; Jennifer Temel; James G Christensen; John C Wain; Thomas J Lynch; Kathy Vernovsky; Eugene J Mark; Michael Lanuti; A John Iafrate; Mari Mino-Kenudson; Jeffrey A Engelman
Journal:  Sci Transl Med       Date:  2011-03-23       Impact factor: 17.956

8.  Personalized oncology through integrative high-throughput sequencing: a pilot study.

Authors:  Sameek Roychowdhury; Matthew K Iyer; Dan R Robinson; Robert J Lonigro; Yi-Mi Wu; Xuhong Cao; Shanker Kalyana-Sundaram; Lee Sam; O Alejandro Balbin; Michael J Quist; Terrence Barrette; Jessica Everett; Javed Siddiqui; Lakshmi P Kunju; Nora Navone; John C Araujo; Patricia Troncoso; Christopher J Logothetis; Jeffrey W Innis; David C Smith; Christopher D Lao; Scott Y Kim; J Scott Roberts; Stephen B Gruber; Kenneth J Pienta; Moshe Talpaz; Arul M Chinnaiyan
Journal:  Sci Transl Med       Date:  2011-11-30       Impact factor: 17.956

9.  Initial genome sequencing and analysis of multiple myeloma.

Authors:  Michael A Chapman; Michael S Lawrence; Jonathan J Keats; Kristian Cibulskis; Carrie Sougnez; Anna C Schinzel; Christina L Harview; Jean-Philippe Brunet; Gregory J Ahmann; Mazhar Adli; Kenneth C Anderson; Kristin G Ardlie; Daniel Auclair; Angela Baker; P Leif Bergsagel; Bradley E Bernstein; Yotam Drier; Rafael Fonseca; Stacey B Gabriel; Craig C Hofmeister; Sundar Jagannath; Andrzej J Jakubowiak; Amrita Krishnan; Joan Levy; Ted Liefeld; Sagar Lonial; Scott Mahan; Bunmi Mfuko; Stefano Monti; Louise M Perkins; Robb Onofrio; Trevor J Pugh; S Vincent Rajkumar; Alex H Ramos; David S Siegel; Andrey Sivachenko; A Keith Stewart; Suzanne Trudel; Ravi Vij; Douglas Voet; Wendy Winckler; Todd Zimmerman; John Carpten; Jeff Trent; William C Hahn; Levi A Garraway; Matthew Meyerson; Eric S Lander; Gad Getz; Todd R Golub
Journal:  Nature       Date:  2011-03-24       Impact factor: 49.962

10.  IDH1 and IDH2 mutations are frequent events in central chondrosarcoma and central and periosteal chondromas but not in other mesenchymal tumours.

Authors:  M Fernanda Amary; Krisztian Bacsi; Francesca Maggiani; Stephen Damato; Dina Halai; Fitim Berisha; Robin Pollock; Paul O'Donnell; Anita Grigoriadis; Tim Diss; Malihe Eskandarpour; Nadège Presneau; Pancras Cw Hogendoorn; Andrew Futreal; Roberto Tirabosco; Adrienne M Flanagan
Journal:  J Pathol       Date:  2011-05-19       Impact factor: 9.883

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  33 in total

Review 1.  Advances in the Molecular Analysis of Soft Tissue Tumors and Clinical Implications.

Authors:  Adrian Marino-Enriquez
Journal:  Surg Pathol Clin       Date:  2015-09

2.  Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma.

Authors:  Shakti H Ramkissoon; Wenya Linda Bi; Steven E Schumacher; Lori A Ramkissoon; Sam Haidar; David Knoff; Adrian Dubuc; Loreal Brown; Margot Burns; Jane B Cryan; Malak Abedalthagafi; Yun Jee Kang; Nikolaus Schultz; David A Reardon; Eudocia Q Lee; Mikael L Rinne; Andrew D Norden; Lakshmi Nayak; Sandra Ruland; Lisa M Doherty; Debra C LaFrankie; Margaret Horvath; Ayal A Aizer; Andrea Russo; Nils D Arvold; Elizabeth B Claus; Ossama Al-Mefty; Mark D Johnson; Alexandra J Golby; Ian F Dunn; E Antonio Chiocca; Lorenzo Trippa; Sandro Santagata; Rebecca D Folkerth; Philip Kantoff; Barrett J Rollins; Neal I Lindeman; Patrick Y Wen; Azra H Ligon; Rameen Beroukhim; Brian M Alexander; Keith L Ligon
Journal:  Neuro Oncol       Date:  2015-03-09       Impact factor: 12.300

Review 3.  Molecular pathologic diagnosis of epidermal growth factor receptor.

Authors:  Cecile L Maire; Keith L Ligon
Journal:  Neuro Oncol       Date:  2014-10       Impact factor: 12.300

4.  Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer.

Authors:  William J Gibson; Daniel T Ruan; Vera A Paulson; Justine A Barletta; Glenn J Hanna; Stefan Kraft; Antonio Calles; Matthew A Nehs; Francis D Moore; Amaro Taylor-Weiner; Jeremiah A Wala; Travis I Zack; Thomas C Lee; Fiona M Fennessy; Erik K Alexander; Tom Thomas; Pasi A Janne; Levi A Garraway; Scott L Carter; Rameen Beroukhim; Jochen H Lorch; Eliezer M Van Allen
Journal:  Clin Cancer Res       Date:  2016-10-17       Impact factor: 12.531

5.  The right drugs at the right time for the right patient: the MD Anderson precision oncology decision support platform.

Authors:  Amber Johnson; Jia Zeng; Ann M Bailey; Vijaykumar Holla; Beate Litzenburger; Humberto Lara-Guerra; Gordon B Mills; John Mendelsohn; Kenna R Shaw; Funda Meric-Bernstam
Journal:  Drug Discov Today       Date:  2015-07-03       Impact factor: 7.851

6.  Institutional implementation of clinical tumor profiling on an unselected cancer population.

Authors:  Lynette M Sholl; Khanh Do; Priyanka Shivdasani; Ethan Cerami; Adrian M Dubuc; Frank C Kuo; Elizabeth P Garcia; Yonghui Jia; Phani Davineni; Ryan P Abo; Trevor J Pugh; Paul van Hummelen; Aaron R Thorner; Matthew Ducar; Alice H Berger; Mizuki Nishino; Katherine A Janeway; Alanna Church; Marian Harris; Lauren L Ritterhouse; Joshua D Campbell; Vanesa Rojas-Rudilla; Azra H Ligon; Shakti Ramkissoon; James M Cleary; Ursula Matulonis; Geoffrey R Oxnard; Richard Chao; Vanessa Tassell; James Christensen; William C Hahn; Philip W Kantoff; David J Kwiatkowski; Bruce E Johnson; Matthew Meyerson; Levi A Garraway; Geoffrey I Shapiro; Barrett J Rollins; Neal I Lindeman; Laura E MacConaill
Journal:  JCI Insight       Date:  2016-11-17

7.  Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer.

Authors:  Emmanuel Rios Velazquez; Chintan Parmar; Ying Liu; Thibaud P Coroller; Gisele Cruz; Olya Stringfield; Zhaoxiang Ye; Mike Makrigiorgos; Fiona Fennessy; Raymond H Mak; Robert Gillies; John Quackenbush; Hugo J W L Aerts
Journal:  Cancer Res       Date:  2017-05-31       Impact factor: 12.701

Review 8.  Molecular Pathogenesis and Diagnostic, Prognostic and Predictive Molecular Markers in Sarcoma.

Authors:  Adrián Mariño-Enríquez; Judith V M G Bovée
Journal:  Surg Pathol Clin       Date:  2016-09

9.  Genetic landscape of metastatic and recurrent head and neck squamous cell carcinoma.

Authors:  Matthew L Hedberg; Gerald Goh; Simion I Chiosea; Julie E Bauman; Maria L Freilino; Yan Zeng; Lin Wang; Brenda B Diergaarde; William E Gooding; Vivian W Y Lui; Roy S Herbst; Richard P Lifton; Jennifer R Grandis
Journal:  J Clin Invest       Date:  2015-11-30       Impact factor: 14.808

Review 10.  Current state of pediatric sarcoma biology and opportunities for future discovery: A report from the sarcoma translational research workshop.

Authors:  Pooja Hingorani; Katherine Janeway; Brian D Crompton; Cigall Kadoch; Crystal L Mackall; Javed Khan; Jack F Shern; Joshua Schiffman; Lisa Mirabello; Sharon A Savage; Marc Ladanyi; Paul Meltzer; Carol J Bult; Peter C Adamson; Philip J Lupo; Rajen Mody; Steven G DuBois; D Williams Parsons; Chand Khanna; Ching Lau; Douglas S Hawkins; R Lor Randall; Malcolm Smith; Poul H Sorensen; Sharon E Plon; Stephen X Skapek; Stephen Lessnick; Richard Gorlick; Damon R Reed
Journal:  Cancer Genet       Date:  2016-04-05
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