Literature DB >> 24071849

The Cancer Genome Atlas Pan-Cancer analysis project.

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.   

Abstract

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

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Year:  2013        PMID: 24071849      PMCID: PMC3919969          DOI: 10.1038/ng.2764

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


  38 in total

Review 1.  The hallmarks of cancer.

Authors:  D Hanahan; R A Weinberg
Journal:  Cell       Date:  2000-01-07       Impact factor: 41.582

2.  Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia.

Authors:  Andrew P Weng; Adolfo A Ferrando; Woojoong Lee; John P Morris; Lewis B Silverman; Cheryll Sanchez-Irizarry; Stephen C Blacklow; A Thomas Look; Jon C Aster
Journal:  Science       Date:  2004-10-08       Impact factor: 47.728

Review 3.  Lessons from the cancer genome.

Authors:  Levi A Garraway; Eric S Lander
Journal:  Cell       Date:  2013-03-28       Impact factor: 41.582

4.  Molecular portraits of human breast tumours.

Authors:  C M Perou; T Sørlie; M B Eisen; M van de Rijn; S S Jeffrey; C A Rees; J R Pollack; D T Ross; H Johnsen; L A Akslen; O Fluge; A Pergamenschikov; C Williams; S X Zhu; P E Lønning; A L Børresen-Dale; P O Brown; D Botstein
Journal:  Nature       Date:  2000-08-17       Impact factor: 49.962

Review 5.  Personalized cancer therapy with selective kinase inhibitors: an emerging paradigm in medical oncology.

Authors:  Ultan McDermott; Jeff Settleman
Journal:  J Clin Oncol       Date:  2009-10-26       Impact factor: 44.544

6.  Mutations of the BRAF gene in human cancer.

Authors:  Helen Davies; Graham R Bignell; Charles Cox; Philip Stephens; Sarah Edkins; Sheila Clegg; Jon Teague; Hayley Woffendin; Mathew J Garnett; William Bottomley; Neil Davis; Ed Dicks; Rebecca Ewing; Yvonne Floyd; Kristian Gray; Sarah Hall; Rachel Hawes; Jaime Hughes; Vivian Kosmidou; Andrew Menzies; Catherine Mould; Adrian Parker; Claire Stevens; Stephen Watt; Steven Hooper; Rebecca Wilson; Hiran Jayatilake; Barry A Gusterson; Colin Cooper; Janet Shipley; Darren Hargrave; Katherine Pritchard-Jones; Norman Maitland; Georgia Chenevix-Trench; Gregory J Riggins; Darell D Bigner; Giuseppe Palmieri; Antonio Cossu; Adrienne Flanagan; Andrew Nicholson; Judy W C Ho; Suet Y Leung; Siu T Yuen; Barbara L Weber; Hilliard F Seigler; Timothy L Darrow; Hugh Paterson; Richard Marais; Christopher J Marshall; Richard Wooster; Michael R Stratton; P Andrew Futreal
Journal:  Nature       Date:  2002-06-09       Impact factor: 49.962

7.  Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma.

Authors:  Nicholas J Wang; Zachary Sanborn; Kelly L Arnett; Laura J Bayston; Wilson Liao; Charlotte M Proby; Irene M Leigh; Eric A Collisson; Patricia B Gordon; Lakshmi Jakkula; Sally Pennypacker; Yong Zou; Mimansa Sharma; Jeffrey P North; Swapna S Vemula; Theodora M Mauro; Isaac M Neuhaus; Philip E Leboit; Joe S Hur; Kyunghee Park; Nam Huh; Pui-Yan Kwok; Sarah T Arron; Pierre P Massion; Allen E Bale; David Haussler; James E Cleaver; Joe W Gray; Paul T Spellman; Andrew P South; Jon C Aster; Stephen C Blacklow; Raymond J Cho
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-17       Impact factor: 11.205

8.  Massive genomic rearrangement acquired in a single catastrophic event during cancer development.

Authors:  Philip J Stephens; Chris D Greenman; Beiyuan Fu; Fengtang Yang; Graham R Bignell; Laura J Mudie; Erin D Pleasance; King Wai Lau; David Beare; Lucy A Stebbings; Stuart McLaren; Meng-Lay Lin; David J McBride; Ignacio Varela; Serena Nik-Zainal; Catherine Leroy; Mingming Jia; Andrew Menzies; Adam P Butler; Jon W Teague; Michael A Quail; John Burton; Harold Swerdlow; Nigel P Carter; Laura A Morsberger; Christine Iacobuzio-Donahue; George A Follows; Anthony R Green; Adrienne M Flanagan; Michael R Stratton; P Andrew Futreal; Peter J Campbell
Journal:  Cell       Date:  2011-01-07       Impact factor: 41.582

9.  Integrated genomic analyses of ovarian carcinoma.

Authors: 
Journal:  Nature       Date:  2011-06-29       Impact factor: 49.962

10.  Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas.

Authors:  Claire Palles; Jean-Baptiste Cazier; Kimberley M Howarth; Enric Domingo; Angela M Jones; Peter Broderick; Zoe Kemp; Sarah L Spain; Estrella Guarino; Estrella Guarino Almeida; Israel Salguero; Amy Sherborne; Daniel Chubb; Luis G Carvajal-Carmona; Yusanne Ma; Kulvinder Kaur; Sara Dobbins; Ella Barclay; Maggie Gorman; Lynn Martin; Michal B Kovac; Sean Humphray; Anneke Lucassen; Christopher C Holmes; David Bentley; Peter Donnelly; Jenny Taylor; Christos Petridis; Rebecca Roylance; Elinor J Sawyer; David J Kerr; Susan Clark; Jonathan Grimes; Stephen E Kearsey; Huw J W Thomas; Gilean McVean; Richard S Houlston; Ian Tomlinson
Journal:  Nat Genet       Date:  2012-12-23       Impact factor: 38.330

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  2000 in total

Review 1.  Next-generation sequencing-based clinical sequencing: toward precision medicine in solid tumors.

Authors:  Toshifumi Wakai; Pankaj Prasoon; Yuki Hirose; Yoshifumi Shimada; Hiroshi Ichikawa; Masayuki Nagahashi
Journal:  Int J Clin Oncol       Date:  2018-12-04       Impact factor: 3.402

2.  Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders.

Authors:  Gregory P Way; Casey S Greene
Journal:  Pac Symp Biocomput       Date:  2018

3.  Pathogenetic Analysis of Sinonasal Teratocarcinosarcomas Reveal Actionable β-catenin Overexpression and a β-catenin Mutation.

Authors:  Andrew C Birkeland; Sarah J Burgin; Megan Yanik; Megan V Scott; Carol R Bradford; Jonathan B McHugh; Scott A McLean; Stephen E Sullivan; Jacques E Nor; Erin L McKean; J Chad Brenner
Journal:  J Neurol Surg B Skull Base       Date:  2017-03-27

4.  Neoantigen Vaccines Pass the Immunogenicity Test.

Authors:  Gerald P Linette; Beatriz M Carreno
Journal:  Trends Mol Med       Date:  2017-08-31       Impact factor: 11.951

5.  Biological Interpretation of Complex Genomic Data.

Authors:  Kathleen M Fisch
Journal:  Methods Mol Biol       Date:  2019

Review 6.  Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer.

Authors:  Yiling Lu; Shiyun Ling; Apurva M Hegde; Lauren A Byers; Kevin Coombes; Gordon B Mills; Rehan Akbani
Journal:  Semin Oncol       Date:  2016-06-15       Impact factor: 4.929

7.  Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing.

Authors:  Yuchao Jiang; Yu Qiu; Andy J Minn; Nancy R Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-29       Impact factor: 11.205

8.  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

9.  A Targeted Quantitative Proteomic Approach Assesses the Reprogramming of Small GTPases during Melanoma Metastasis.

Authors:  Ming Huang; Tianyu F Qi; Lin Li; Gao Zhang; Yinsheng Wang
Journal:  Cancer Res       Date:  2018-08-02       Impact factor: 12.701

10.  miR30a inhibits LOX expression and anaplastic thyroid cancer progression.

Authors:  Myriem Boufraqech; Naris Nilubol; Lisa Zhang; Sudheer Kumar Gara; Samira M Sadowski; Amit Mehta; Mei He; Sean Davis; Jennifer Dreiling; John A Copland; Robert C Smallridge; Martha M Quezado; Electron Kebebew
Journal:  Cancer Res       Date:  2014-12-08       Impact factor: 12.701

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