Topics Covered
- Major Cancer Genomic Studies and Data Portals
- Other Genetics Data Resources
- Specialized Databases for Genomic Analyses
- Analytical Programming Packages for Cancer Genomic Datasets
- Cloud Resources with Available Cancer Genomic Datasets
- “Awesome Bioinformatics” Resources
Practical
- Using popular portals to answer research questions:
- cBioPortal
- FIREBROWSE
- GTEx
- ICGC Portal
- Visualizing mutation data
In this session we will provide an overview of current cancer genomic studies and many common genetic resources. We will begin by highlighting major cancer genomics studies (e.g. TCGA, ICGC, PCAWG, Genomics England, MSK-IMPACT, GENIE) and their associated data portals such as cBioPortal, FIREBROWSE, GDC and more, plus genetics databases useful for genomic analyses in general such as Ensembl, 1000 genomes, gnomAD, etc.
Then we will highlight various resources for more in-depth cancer genomics analysis such as platforms for driver gene analysis (IntOGen), mutational signature analysis (mSigPortal, Signal, COSMIC), TCGA somatic analysis (FIREBROWSE), PCAWG somatic analysis, and other specific analysis platforms (e.g. alternative splicing, noncoding, IPA). Finally we’ll conclude the lecture section by highlighting databases with programmatic access, several cloud-based analysis resources, and the “Awesome Bioinformatics” resources.
The practical section will provide an opportunity to practice using most of these resources and data portals to answer cancer research questions.