Cancer Genome Computational Analysis

Skip to main content Broad Institute BROAD INSTITUTE CareersGivingIntranet Search ABOUT US ABOUT US This is Broad History Leadership Partner Institutions and Community Director's Page Administration Partnering and Licensing #WhyIScience JOIN US Careers at Broad PEOPLE FOUNDERS BOARD OF DIRECTORS BOARD OF SCIENTIFIC COUNSELORS LEADERSHIP Institute Leadership Institute Members Institute Scientists Associate Members Program and Platform Directors STAFF Senior Professional Scientists Directory SCIENCE PUBLICATIONS LABS SCIENTIFIC AREAS Chemical Biology and Therapeutics Science Drug Discovery (CDoT) Genome Regulation, Cellular Circuitry and Epigenomics Immunology Medical and Population Genetics Metabolism TECHNOLOGY AREAS Data Sciences Genetic Perturbation Genomics Imaging Metabolomics Proteomics DISEASE AREAS Cancer Cardiovascular Disease Diabetes Infectious Disease and Microbiome Kidney Disease Obesity Psychiatric Disease Rare Disease DATA AND TOOLS DATA SCIENCES FREQUENTLY USED Drug Repurposing Hub GATK Hail IGV Terra Tumor Portal SEARCH DATA, SOFTWARE AND TOOLS CENTERS CARLOS SLIM CENTER FOR HEALTH RESEARCH GERSTNER CENTER FOR CANCER DIAGNOSTICS KLARMAN CELL OBSERVATORY MERKIN INSTITUTE STANLEY CENTER FOR PSYCHIATRIC RESEARCH COMMUNITY FOR EDUCATORS Educational Tours Summer Research Programs Classroom Resources Inside Broad: Take a video tour FOR SCIENTISTS Technical Workshops BroadE GTEx GATK Fellowships Leaders in Data Science Models, Inference & Algorithms FOR STUDENTS Summer Research Programs MIT UROP Program Post-Baccalaureate Program Science Writing and Communications Internship ART AND SCIENCE CONNECTION FOR THE PUBLIC Broad@15 Count Me In Informing Discussion on Policy Issues Midsummer Nights Science Next Generation in Biomedicine Symposium Rare Disease Day Science for All Seasons COVID-19 TESTING Areas of need College and university screening Questions about testing CONTACT CONTACT US DIRECTORY NEWS AND MEDIA NEWS FROM BROAD News Broadminded Blog Podcast Visuals PRESS ROOM For Journalists Media Resources Embargo Policy VIDEOS KEY TOPICS COVID-19 CRISPR HCA Schizophrenia YOU ARE HERE HOME » SCIENCE » DISEASE AREAS » CANCER CANCER GENOME COMPUTATIONAL ANALYSIS The Cancer Genome Computational Analysis (CGCA) group — a central component of the Broad Institute’s Cancer Program — addresses unanswered questions of cancer biology and genomics through the development of computational methods and tools, in conjunction with platforms, datasets and resources. Specifically, the group works to understand cancer by characterizing and interpreting genomic data: Characterization: fully describing the genomic events (including somatic and germline events, at DNA, RNA, and proteomic levels) in tumor and normal samples coming from individual patients Interpretation: analysis of characterization data across populations or cohorts with the aims of identifying a) genes, regions, and pathways that are altered beyond what is expected by chance, and b) subtypes of disease CGCA works closely with many groups within the Broad, including the institute’s Genomics, Genetic Perturbation, and Data Sciences platforms. CGCA members also engage with collaborators from the Broad’s partner institutions and outside organizations such as IBM. The team also participates in several National Institutes of Health-funded national consortia, such as The Cancer Genome Atlas (TCGA), the Genomic Data Analysis Network, the Clinical Proteomic Tumor Analysis Consortium, the Genotype-Tissue Expression (GTEx) Consortium. The CGCA team has created a number of powerful genomic analysis tools and platforms for the cancer research community, including: FireCloud, a cloud-based cancer genomics analysis platform developed with the Broad’s Data Science Platform. FireCloud houses the full dataset set generated by TCGA and a suite of robust cancer genomics workflows containing CGCA-developed tools, such as: D-ToxoG GISTIC MuTECT Oncotator ABSOLUTE, which estimates purity/ploidy, and computes absolute copy-number and mutation multiplicities. dRanger, a tool for identifying somatic rearrangements as clusters of aberrant paired-end sequencing reads in a tumor sample. Mutsig, which identifies genes in a dataset that have mutated more often than would expected by chance. POLYSOLVER, which infers HLA types from whole exome sequence data. CGCA has also built and maintains several key genomic data resources, such as: TumorPortal, a comprehensive mutational dataset comprising exome mutation data from 21 cancer types FireBrowse, a user-friendly, web-based entry point to downloadable TCGA datasets, summary reports, and graphical tools. FireBrowse sits atop TCGA GDAC Firehose, an application providing access to TCGA datasets and a robust selection of tools and pipelines for analyzing cancer genome data, as well as thousands of data analysis archives. GTEx Portal, a comprehensive atlas and open database of gene expression and gene regulation across human tissues that provides a “normal” dataset against which to compare tumor-based expression and regulation data. 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