CANB 610:Materials

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Revision as of 23:44, 2 February 2012

• • 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

1. Guo G, Gui Y, Gao S, Tang A, Hu X, Huang Y, Jia W, Li Z, He M, Sun L, Song P, Sun X, Zhao X, Yang S, Liang C, Wan S, Zhou F, Chen C, Zhu J, Li X, Jian M, Zhou L, Ye R, Huang P, Chen J, Jiang T, Liu X, Wang Y, Zou J, Jiang Z, Wu R, Wu S, Fan F, Zhang Z, Liu L, Yang R, Liu X, Wu H, Yin W, Zhao X, Liu Y, Peng H, Jiang B, Feng Q, Li C, Xie J, Lu J, Kristiansen K, Li Y, Zhang X, Li S, Wang J, Yang H, Cai Z, and Wang J. . pmid:22138691. PubMed HubMed [Guo]

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
• Image: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

2. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, and Wigler M. . pmid:21399628. PubMed HubMed [Navin]

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

Lecture slides

Week 3: RNA sequencing

Papers

3. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, and Cheung VG. . pmid:21596952. PubMed HubMed [Li-2011]
4. Paz N, Levanon EY, Amariglio N, Heimberger AB, Ram Z, Constantini S, Barbash ZS, Adamsky K, Safran M, Hirschberg A, Krupsky M, Ben-Dov I, Cazacu S, Mikkelsen T, Brodie C, Eisenberg E, and Rechavi G. . pmid:17908822. PubMed HubMed [RNA_Editing_in_cancer]
5. Langmead B, Trapnell C, Pop M, and Salzberg SL. . pmid:19261174. PubMed HubMed [bowtie]
6. Trapnell C, Pachter L, and Salzberg SL. . pmid:19289445. PubMed HubMed [tophat]
7. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, and Pachter L. . pmid:20436464. PubMed HubMed [cufflinks]

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

Week 4: Functional Genomics

Papers

11. Possemato R, Marks KM, Shaul YD, Pacold ME, Kim D, Birsoy K, Sethumadhavan S, Woo HK, Jang HG, Jha AK, Chen WW, Barrett FG, Stransky N, Tsun ZY, Cowley GS, Barretina J, Kalaany NY, Hsu PP, Ottina K, Chan AM, Yuan B, Garraway LA, Root DE, Mino-Kenudson M, Brachtel EF, Driggers EM, and Sabatini DM. . pmid:21760589. PubMed HubMed [possemato-2011]
12. Premsrirut PK, Dow LE, Kim SY, Camiolo M, Malone CD, Miething C, Scuoppo C, Zuber J, Dickins RA, Kogan SC, Shroyer KR, Sordella R, Hannon GJ, and Lowe SW. . pmid:21458673. PubMed HubMed [background]

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)

Bonus Materials

Lecture slides

Week 5: TBA

Papers

Bonus Materials

Lecture slides

Week 6: Chromothripsis

Papers

13. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, and Campbell PJ. . pmid:21215367. PubMed HubMed [Stephens-2011]

Bonus Materials

link to Cell podcast by the author

Lecture Slides

Week 7: Circadian

Papers

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

Bonus Materials

• Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage. http://www.ncbi.nlm.nih.gov/pubmed/20649466
• Does evening sun increase the risk of skin cancer? http://www.ncbi.nlm.nih.gov/pubmed/22084098

Week 8: TBA

Papers

14. = [pmid]

Bonus Materials

Week 9: TBA

Papers

14. = [pmid]

Bonus Materials

Week 10: TBA

Papers

14. = [pmid]

Bonus Materials

Week 11: TBA

Papers

14. = [pmid]

Bonus Materials