The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and discover major cancer-causing genomic alterations to create a comprehensive “atlas” of cancer genomic profiles. So far, TCGA researchers have analysed large cohorts of over 30 human tumours through large-scale genome sequencing and integrated multi-dimensional analyses. Studies of individual cancer types, as well as comprehensive pan-cancer analyses have extended current knowledge of tumorigenesis. A major goal of the project was to provide publicly available datasets to help improve diagnostic methods, treatment standards, and finally to prevent cancer. This review discusses the current status of TCGA Research Network structure, purpose, and achievements.

[1]  P. Laurén,et al.  THE TWO HISTOLOGICAL MAIN TYPES OF GASTRIC CARCINOMA: DIFFUSE AND SO-CALLED INTESTINAL-TYPE CARCINOMA. AN ATTEMPT AT A HISTO-CLINICAL CLASSIFICATION. , 1965, Acta pathologica et microbiologica Scandinavica.

[2]  H. Bartsch,et al.  International Agency for Research on Cancer. , 1969, WHO chronicle.

[3]  F. Sanger,et al.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. , 1975, Journal of molecular biology.

[4]  K. Kinzler,et al.  Genetic instabilities in human cancers , 1998, Nature.

[5]  A. Jemal,et al.  Global cancer statistics , 2011, CA: a cancer journal for clinicians.

[6]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[7]  W. Marston Linehan,et al.  Genetic Basis of Cancer of the Kidney , 2004, Clinical Cancer Research.

[8]  Sergio Ricci,et al.  Long-term survival results of a randomized trial comparing gemcitabine plus cisplatin, with methotrexate, vinblastine, doxorubicin, plus cisplatin in patients with bladder cancer. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[9]  G. Mills,et al.  Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells , 2006, Molecular Cancer Therapeutics.

[10]  H. Bayley,et al.  Sequencing single molecules of DNA. , 2006, Current opinion in chemical biology.

[11]  Joshua M. Korn,et al.  Integrated detection and population-genetic analysis of SNPs and copy number variation , 2008, Nature Genetics.

[12]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[13]  Joshua M. Korn,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.

[14]  Jonas S. Almeida,et al.  RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays , 2008, BMC Bioinformatics.

[15]  S. Nishizuka,et al.  Reverse-phase protein lysate microarrays for cell signaling analysis , 2008, Nature Protocols.

[16]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[17]  Lawrence Lum,et al.  Small molecule-mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer , 2008, Nature chemical biology.

[18]  M. Stratton,et al.  The cancer genome , 2009, Nature.

[19]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[20]  J. Uhm Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2009 .

[21]  T. Dale,et al.  A useful approach to identify novel small-molecule inhibitors of Wnt-dependent transcription. , 2010, Cancer research.

[22]  Subha Madhavan,et al.  The Cancer Genome Workbench: Identifying and Visualizing Complex Genetic Alterations in Tumors , 2010 .

[23]  R. Wilson,et al.  Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. , 2010, Cancer cell.

[24]  P. Laird Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.

[25]  Wei Huang,et al.  Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship , 2010, Proceedings of the National Academy of Sciences.

[26]  I. Pe’er,et al.  Allelic Selection of Amplicons in Glioblastoma Revealed by Combining Somatic and Germline Analysis , 2010, PLoS genetics.

[27]  C. Mathers,et al.  Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008 , 2010, International journal of cancer.

[28]  L. Chin,et al.  Glioma oncoprotein Bcl2L12 inhibits the p53 tumor suppressor. , 2010, Genes & development.

[29]  L. Chin,et al.  Mig-6 controls EGFR trafficking and suppresses gliomagenesis , 2010, Proceedings of the National Academy of Sciences.

[30]  R. Karchin,et al.  Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. , 2011, Cancer research.

[31]  D. Scudiero,et al.  S100A4-induced cell motility and metastasis is restricted by the Wnt/β-catenin pathway inhibitor calcimycin in colon cancer cells , 2011, Molecular biology of the cell.

[32]  Benjamin J. Raphael,et al.  Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.

[33]  Tian-Li Wang,et al.  Amplification of The ch19p13.2 NACC1 Locus in Ovarian High-grade Serous Carcinoma , 2010, Modern Pathology.

[34]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[35]  R. Garzon,et al.  Potential applications of microRNAs in cancer diagnosis, prognosis, and treatment. , 2011, Seminars in oncology.

[36]  Thomas Tuschl,et al.  miRNAs in human cancer , 2011, The Journal of pathology.

[37]  K. Hess,et al.  Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. , 2011, JAMA.

[38]  Jannik N. Andersen,et al.  Cancer genomics: from discovery science to personalized medicine , 2011, Nature Medicine.

[39]  Mary Goldman,et al.  The UCSC cancer genomics browser: update 2011 , 2010, Nucleic Acids Res..

[40]  D. Brat,et al.  Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma , 2012, Science.

[41]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of human colon and rectal cancer , 2012, Nature.

[42]  Gord Glendon,et al.  Association Between BRCA1 and BRCA2 Mutations and Survival in Women With Invasive Epithelial Ovarian Cancer , 2012 .

[43]  Steven J. M. Jones,et al.  Comprehensive genomic characterization of squamous cell lung cancers , 2012, Nature.

[44]  Cristian Coarfa,et al.  miRNA data analysis: next-gen sequencing. , 2012, Methods in molecular biology.

[45]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[46]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[47]  Adam A. Margolin,et al.  Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas , 2013, Nature Genetics.

[48]  S. Madhavan,et al.  Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse , 2013, Front. Genet..

[49]  Jun Li,et al.  TCPA: a resource for cancer functional proteomics data , 2013, Nature Methods.

[50]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of clear cell renal cell carcinoma , 2013, Nature.

[51]  Stephen M. Moore,et al.  The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository , 2013, Journal of Digital Imaging.

[52]  T. Samuelsson,et al.  The landscape of viral expression and host gene fusion and adaptation in human cancer , 2013, Nature Communications.

[53]  Jacques Ferlay,et al.  GLOBOCAN 2012 v1.0, Cancer Incidence and Mortality Worldwide: IARC Cancer Base No. 11 [Internet] , 2013 .

[54]  Thomas Tuschl,et al.  MicroRNAs in human cancer. , 2013, Advances in experimental medicine and biology.

[55]  Nuria Lopez-Bigas,et al.  Visualizing multidimensional cancer genomics data , 2013, Genome Medicine.

[56]  D. Wheeler,et al.  Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif , 2013, Nature Communications.

[57]  Benjamin J. Raphael,et al.  Mutational landscape and significance across 12 major cancer types , 2013, Nature.

[58]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[59]  Parantu K. Shah,et al.  canEvolve: A Web Portal for Integrative Oncogenomics , 2013, PloS one.

[60]  Bahram Parvin,et al.  Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association , 2013, IEEE Transactions on Medical Imaging.

[61]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[62]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[63]  Chris Sander,et al.  Emerging landscape of oncogenic signatures across human cancers , 2013, Nature Genetics.

[64]  Benjamin J. Raphael,et al.  Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. , 2013, The New England journal of medicine.

[65]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[66]  Gary D. Bader,et al.  The mutational landscape of phosphorylation signaling in cancer , 2013, Scientific Reports.

[67]  Gary D Bader,et al.  Comprehensive identification of mutational cancer driver genes across 12 tumor types , 2013, Scientific Reports.

[68]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[69]  D. Haussler,et al.  The Somatic Genomic Landscape of Glioblastoma , 2013, Cell.

[70]  Joel H. Saltz,et al.  Research and applications: Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data , 2013, J. Am. Medical Informatics Assoc..

[71]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[72]  Steven J. M. Jones,et al.  Integrated genomic characterization of endometrial carcinoma , 2013, Nature.

[73]  Benjamin J. Raphael,et al.  Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin , 2014, Cell.

[74]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of gastric adenocarcinoma , 2014, Nature.

[75]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.

[76]  Jingchun Zhu,et al.  Realizing the Promise of Reverse Phase Protein Arrays for Clinical, Translational, and Basic Research: A Workshop Report , 2014, Molecular & Cellular Proteomics.

[77]  The Cancer Genome Atlas Research Network Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.

[78]  Mary Goldman,et al.  The UCSC Cancer Genomics Browser: update 2015 , 2014, Nucleic Acids Res..