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Meyerson Lab - Cancer Genomics and Genome-Inspired Discovery

Meyerson Laboratory
CANCER GENOMICS AND GENOME-INSPIRED DISCOVERY

Datasets, Portals and Tools

Useful Cancer Genomics Data Portals and Sites:
  • Broad Institute TCGA copy number portal: Links to copy number profiles for over 10,000 cancers.
    • The Integrative Genomics Viewer (IGV) is the browser. Data used in Zack et al., Nature Genetics, 2013, and multiple TCGA cancer marker papers.
    • Tumorscape: Data for Beroukhim et al., Nature, 2010 with copy number profiles for ~3,000 cancers, now available within the Broad copy number portal, under '2011-02-01 Tumorscape'.
  • Tumorportal: Website with cancer mutation data for over 4,000 cancers, from Lawrence et al., Nature, 2014.
  • ​TCGA central data portal
  • dbGAP: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000568.v1.p1​
  • GTEx: http://www.gtexportal.org/home/
  • COSMIC: http://cancer.sanger.ac.uk/cosmic
  • DepMap: https://depmap.org/portal/​
  • Gene Pattern: http://www.broadinstitute.org/cancer/software/genepattern/
  • ​cBioPortal: http://www.cbioportal.org/
  • International Cancer Genome Consortium: https://icgc.org/
  • The Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geo/
  • The UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgGateway
  • Genomic Data Commons: home page and data portal
Meyerson Lab Tools
  • virID: https://github.com/jnoms/virID
  • ASCETS: https://github.com/beroukhim-lab/ascets
  • GATK PathSeq: All GATK tools available here

Meyerson Lab Datasets for Pathogen Discovery Projects:
  • Cord colitis: http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP018116​
  • Colon genome discovery (16S rRNA sequences from human colon samples): http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000383

Meyerson Lab Datasets for Cancer Genome Analysis Projects:
  • Pugh et al., Pleuropulmonary Blastoma: http://www.ncbi.nlm.nih.gov/bioproject/17411
  • Ojesina et al., Cervical Cancer: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000600.v1.p1
  • Neuroblastoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000467.v8.p1
  • Medulloblastoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000504.v2.p2
  • Carcinoid: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000579.v1.p1
  • Imielinski et al., Lung Adenocarcinoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000488.v2.p1
  • Banerji et al., Breast Cancer: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000369.v1.p1​
  • Metastatic Cancers:
    https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001417.v2.p1
  • Pediatric Renal Medullary Carcinomas
    https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001800.v2.p1
  • Castration Resistant Prostate Cancer​http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001577.v1.p1
  • ​Neuroendocrine Tumors
    https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000579.v1.p1
  • Solitary Fibrous Tumors
    https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000568.v1.p1

Citations of the above images
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