CANB 610:Materials

• • IN PROGRESS**

Class Focus, Winter 2012

1. Organization Meeting and Rules of Engagement
2. Genomics and Cancer
3. Genomic instability and Cancer
4. Drug Discovery

Organizational Meeting: Introduction and Scheduling

Presentation Zen

1. Slide Zen
2. Delivery Zen
3. Feel free to add links that help you

Evaluation Forms

• Evaluation Form MC
• Evaluation Form Presenter 1(Intro)
• Evaluation Form Presenter 2
• Dept. Evaluation Form

Week 1: Tumor Sequencing, part 1

Papers

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Bonus Materials

• Kidney cancer http://www.ncbi.nlm.nih.gov/pubmed/20368728
• Mutations in cancer http://www.ncbi.nlm.nih.gov/pubmed/17932254
• Hallmarks of cancer http://www.ncbi.nlm.nih.gov/pubmed/21376230
• Sequencing technologies http://www.ncbi.nlm.nih.gov/pubmed/20847746

and then a bit of a leap:

• Application to clinic http://www.ncbi.nlm.nih.gov/pubmed/22133722

Lecture Slides

• ion torrent video
• File:Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway.pptx
• Lectures on genomics 13 week Series on Genomics 2012 on YouTube
• Spectra of Somatic Mutations Michael Lawrence lecture from 2011 TCGA conference on somatic mutation heterogeneity

Week 2: Tumor Sequencing, part 2

Papers

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Bonus Materials

• Previous work from Wigler on progression http://www.ncbi.nlm.nih.gov/pubmed/19903760
• Old work on heterogeneity http://www.ncbi.nlm.nih.gov/pubmed/9108466
• Evolution by serial sampling http://www.ncbi.nlm.nih.gov/pubmed/20393555
• Evolution in pancreatic cancer http://www.ncbi.nlm.nih.gov/pubmed/20981101
• Mathematical treatment of rearrangement phylogeny (suggested by Paul) http://www.ncbi.nlm.nih.gov/pubmed/21994251
• Michor (suggested by Paul) http://www.ncbi.nlm.nih.gov/pubmed/20864632

• Taniguchi paper on BRCA2 compensatory mutations following cisplatin http://www.ncbi.nlm.nih.gov/pubmed/18264087
• Ashworth paper on BRCA2 compensatory mutations in Ovarian cancer following PARPi http://www.ncbi.nlm.nih.gov/pubmed/18264088

Week 3: RNA sequencing

Papers

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Bonus Materials

8. Very Few RNA and DNA Sequence Differences in the Human Transcriptome http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025842

9. Post on Paralogs and Splice Junctions http://www.genomesunzipped.org/2011/05/notes-on-the-evidence-for-extensive-rna-editing-in-humans.php

10. nice pictures for presentations http://www.sciencephoto.com/search?subtype=keywords&searchstring=transcription&oldsearchstring=ribosome&matchtype=&sort_results=&media_type=images&license=all&channel=all&Search.x=0&Search.y=0

Lecture Slides

• Widespread RNA and DNA differences

Week 4: Functional Genomics

Papers

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http://www.nature.com/nrc/journal/v11/n9/full/nrc3128.html Jones, R. G. & Thompson, C. B. Tumor suppressors and cell metabolism: a recipe for cancer growth.Genes Dev. 23, 537–548 (2009)

Lecture slides

Introduction: Cancer Metabolism, Functional Genomics, and Breast Cancer
Results: Functional Genomics Reveal that the Serine Synthesis Pathway is Essential in Breast Cancer

General Background for Genomic Instability and Cancer

• The DNA damage response and cancer therapy http://www.ncbi.nlm.nih.gov/pubmed/22258607
• Defining 'chromosomal instability'. http://www.ncbi.nlm.nih.gov/pubmed/18192061

Week 6: Chromothripsis

Papers

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Bonus Materials

link to Cell podcast by the author

Week 7: Circadian rhythm and cancer

Papers

• Control of skin cancer by the circadian rhythm http://www.ncbi.nlm.nih.gov/pubmed/22025708

Bonus Materials

• Does evening sun increase the risk of skin cancer? http://www.ncbi.nlm.nih.gov/pubmed/22084098
• Circadian clock control of the cellular response to DNA damage http://www.ncbi.nlm.nih.gov/pubmed/20227409
• Circadian rhythms and tumor growth http://www.ncbi.nlm.nih.gov/pubmed/22252116
• Circadian Integration of Metabolism and Energetics http://www.ncbi.nlm.nih.gov/pubmed/21127246
• The genetics of mammalian circadian order and disorder: implications for physiology and disease http://www.ncbi.nlm.nih.gov/pubmed/18802415
  
• Circadian timing in cancer treatment http://www.ncbi.nlm.nih.gov/pubmed/20055686

Presentations

• Introduction:Control of skin cancer by the circadian rhythm
• Results: Control of skin cancer by the circadian rhythm

Week 8: Inflammation and cancer

Papers

• The Mutyh Base Excision Repair Gene Influences the Inflammatory Response in a Mouse Model of Ulcerative Colitis http://www.ncbi.nlm.nih.gov/pubmed/20706593
• DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice. http://www.ncbi.nlm.nih.gov/pubmed/18521188

Bonus Materials

• Base Excision Repair and Lesion-Dependent Subpathways for Repair of Oxidative DNA Damage http://www.ncbi.nlm.nih.gov/pubmed/20649466
• Intestinal Inflammation and Cancer http://www.ncbi.nlm.nih.gov/pubmed/21530747

Lecture Slides

• Background: Inflammation and Cancer

Week 9: Drug Development part 1 GIST

Papers

• ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours http://www.nature.com/nature/journal/v467/n7317/full/nature09409.html

Bonus Materials

See supplemental materials including excel spreadsheets and movies that accompany the main paper

• Cancer: Oncogenes in context. http://www.nature.com/nature/journal/v467/n7317/full/467796a.html

Lecture Slides

• Introduction: GI Stromal Tumors and ETV1
• Results: GIST and ETV1

Week 11: Drug Development part 2

Papers

• The secret ally: immunostimulation by anticancer drugs. http://www.ncbi.nlm.nih.gov/pubmed/22301798