The Cancer Genome Atlas TCGA and c Bio

The Cancer Genome Atlas (TCGA) and c. Bio. Portal Nitish Mishra

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), micro. RNA profiling, proteomics (RPPA), and chromatin accessibility (ATAC-seq) • TCGA have published ~70 research articles. • There are 3554 authorized requesters associated with TCGA study (currently)

Number of publications by using TCGA Pubmed - The Cancer Genome Atlas (TCGA) on 20 th Sep 2019 1200 1144 930 1000 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

Webserver based on TCGA • https: //www. cbioportal. org/ (c. Bio. Portal) • http: //gepia. cancer-pku. cn/ (GEPIA) • https: //biit. cs. ut. ee/methsurv/ (Meth. Surv) • https: //hgserver 1. amc. nl/cgi-bin/r 2/main. cgi (R 2 gene) • https: //xenabrowser. net/datapages/ (Xena) • https: //www. proteinatlas. org/ (The Human Protein Atlas) • https: //cptac-data-portal. georgetown. edu/cptac. Public/ (CPTAC)

R packages for TCGA data analysis • TCGAbiolinks (https: //github. com/Bioinformatics. FMRP/TCGAbiolinks) • RTCGAToolbox (https: //github. com/mksamur/RTCGAToolbox) • Genomic. Data. Commons (https: //github. com/Bioconductor/Genomic. Data. Commons) • GDCRNATools (https: //github. com/Jialab-UCR/GDCRNATools) • cgdsr (https: //github. com/c. Bio. Portal/cgdsr) c. Bio. Portal