Understanding the Cancer Genome Atlas (TCGA) Project

The Cancer Genome Atlas (TCGA) project, initiated in 2005, aims to identify genetic mutations in cancer through genome sequencing. Supervised by the Center for Cancer Genomics, TCGA has expanded over the years, publishing numerous research articles and involving various tumor types. The project has led to significant contributions in understanding cancer genetics and has a wide range of applications in cancer research.

• Cancer
• Genome
• Research
• TCGA
• Genetics

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1. The Cancer Genome Atlas (TCGA) and The Cancer Genome Atlas (TCGA) and cBioPortal cBioPortal Nitish Mishra

2. TCGA history TCGA history TCGA is a project, begun in 2005, to catalogue genetic mutations responsible for cancer, using genome sequencing. TCGA is supervised by the Center for Cancer Genomics and the National Human Genome Research Institute. A three-year pilot project, begun in 2006, focused on characterization of three types of human cancers: glioblastoma, lung, and ovarian cancer. In 2009, it expanded into phase II, which planned to complete the genomic characterization and sequence analysis of 20 25 different tumor types by 2014 Gene expression (RNA-seq and array), copy number variation (array and genome sequencing), SNP genotyping (GGS and WES), DNA methylation (array and RBSS), microRNA profiling, proteomics (RPPA), and chromatin accessibility (ATAC-seq) TCGA have published ~70 research articles. There are 3554 authorized requesters associated with TCGA study (currently)

3. Number of publications by using TCGA Number of publications by using TCGA Pubmed - The Cancer Genome Atlas (TCGA) on 20thSep 2019 1200 1144 1000 930 800 646 600 461 400 313 170 200 113 45 26 10 7 2 2 0 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007

5. Project TCGA-BRCA TCGA-GBM TCGA-OV TCGA-LUAD TCGA-UCEC TCGA-KIRC TCGA-HNSC TCGA-LGG TCGA-THCA TCGA-LUSC TCGA-PRAD TCGA-SKCM TCGA-COAD TCGA-STAD TCGA-BLCA TCGA-LIHC TCGA-CESC TCGA-KIRP TCGA-SARC TCGA-LAML TCGA-ESCA TCGA-PAAD TCGA-PCPG TCGA-READ TCGA-TGCT TCGA-THYM TCGA-KICH TCGA-ACC TCGA-MESO TCGA-UVM TCGA-DLBC TCGA-UCS TCGA-CHOL Cases Seq Exp SNV CNV Meth Clinical Clinical Supplement 1,098 617 608 585 560 537 528 516 507 504 500 470 461 443 412 377 307 291 261 200 185 185 179 172 150 124 113 1,098 617 608 585 560 537 528 516 507 504 500 470 461 443 412 377 307 291 261 200 185 185 179 172 150 124 113 1,098 406 575 582 559 535 528 516 507 504 498 470 460 443 412 377 307 291 261 195 185 185 179 171 150 124 1,097 166 492 519 559 534 528 516 507 504 498 469 459 439 412 376 307 291 261 188 184 178 179 167 150 124 1,044 396 443 569 542 339 510 513 496 497 498 470 433 441 412 375 305 288 255 149 184 183 179 158 150 123 1,098 599 597 518 558 534 526 515 505 504 498 470 460 443 412 376 302 290 261 200 185 185 179 167 150 124 1,095 423 602 579 559 533 528 516 507 503 498 470 458 443 412 377 307 291 261 140 185 184 179 165 150 124 1,098 617 608 585 560 537 528 516 507 504 500 470 461 443 412 377 307 291 261 200 185 185 179 172 150 124 113 66 92 87 80 48 57 51 66 80 87 80 48 57 36 66 92 83 80 37 57 51 66 92 87 80 50 57 36 66 80 87 80 48 57 36 92 87 80 58 57 51 92 87 80 58 57 51 92 87 80 58 57 51 11,315 10,999 10,558 10,418 11,124 10,943 11,315 11,315

6. Webserver based on TCGA https://www.cbioportal.org/ (cBioPortal) http://gepia.cancer-pku.cn/ (GEPIA) https://biit.cs.ut.ee/methsurv/ (MethSurv) https://hgserver1.amc.nl/cgi-bin/r2/main.cgi (R2 gene) https://xenabrowser.net/datapages/ (Xena) https://www.proteinatlas.org/ (The Human Protein Atlas) https://cptac-data-portal.georgetown.edu/cptacPublic/ (CPTAC)

7. R packages for TCGA data analysis TCGAbiolinks (https://github.com/BioinformaticsFMRP/TCGAbiolinks) RTCGAToolbox (https://github.com/mksamur/RTCGAToolbox) GenomicDataCommons (https://github.com/Bioconductor/GenomicDataCommons) GDCRNATools (https://github.com/Jialab-UCR/GDCRNATools) cgdsr (https://github.com/cBioPortal/cgdsr) cBioPortal