Bioinformatics for Cancer Genomics

Course Objectives
Course Material
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Module 1: Introduction to cancer genomics (Faculty: John McPherson)
Content:
- Overview of cancer genomics field
- Common applications of HT technologies in cancer genomics
- {"title"=>"Concepts and case studies of cancer genomics from the literature", "content"=>["Cancer genetics", "Pharmacogenomics", "Diagnostic vs. prognostic markers and druggable targets"]}
- Data security and privacy
Presentation file(s):
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Module 2: Visualizing Cancer Genomic Data (Faculty: Francis Ouellette)
Content:
- {"title"=>"Overview of cancer specific databases, as well genome browsing and cancer genome browsing. The databases:", "content"=>["ICGC portal, TCAG, etc.", "COSMIC, dbSNP, etc."]}
- {"title"=>"The browser tools:", "content"=>["IGV", "UCSC"]}
Presentation file(s):
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Module 3: Gene Expression Profiling (Faculty: Paul Boutros)
Content:
- What is involved in mapping reads to a reference genome
- What are the FASTQ and SAM/BAM file formats
- Some common terminology used to describe alignments
- Fundamentals of de novo assembly
- Data structures used by assemblers (de Bruijn graphs and overlap graphs)
- Common steps that assemblers perform
- Overview of commonly used software
Presentation file(s):
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Module 4: Genome Rearrangements (Faculty: Paul Medvedev)
Content:
- Importance of copy number alterations in cancer
- Methods for detecting copy number alterations
- Tools for evaluating CNAs in HT-seq data
Presentation file(s):
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Module 5: Copy Number Alterations (Faculty: Sohrab Shah)
Content:
- Relevance of detecting somatic mutations in cancer genomics
- Strategies for detection of somatic mutations and factors considered by SNV callers
- Binomial mixture models to model allelic counts
- Simultaneous analysis of tumor and normal data
- Sources of artifacts and false positives
Presentation file(s):
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Module 6: Somatic Mutations (Faculty: Sohrab Shah)
Content:
- Role of gene expression profiles in the cancer continuum
- {"title"=>"The Technology Platform: High-throughput sequencing", "content"=>["Variety of platforms and their differences", "Experimental design considerations", "Limitations of experiments"]}
- {"title"=>"The Analysis Tools:", "content"=>["Outline of a RNA-Seq analysis pipeline", "Tools for analysis of RNA-Seq data"]}
Presentation file(s):
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Module 7: Pathway Analysis & Biological Intepretation (Faculty: Gary Bader)
Content:
- Genomic rearrangement and its effect on the transcriptome
- Biological relevance of gene fusions in cancer biology
- {"title"=>"The technology platform: RNA-Seq", "content"=>["Overview of the RNA-Seq protocol", "Experimental design considerations"]}
- {"title"=>"The analysis tools:", "content"=>[{"title"=>"Alignment based fusion discovery", "content"=>["Paired end RNA-Seq alignments and gene fusion evidence", "Discerning true fusions from artifacts"]}, {"title"=>"Assembly based fusion discovery", "content"=>["Benefits/drawbacks of assembly methods", "Identifying gene fusions from RNA-Seq assemblies"]}]}
- Clinical applications
Presentation file(s):
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Module 8: Integration of Clinical Data (Faculty: Anna Lapuk)