CANB 610:Materials

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	==Week 5: No Class==		==Week 5: No Class==
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	*The DNA damage response and cancer therapy http://www.ncbi.nlm.nih.gov/pubmed/22258607		*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		*Defining 'chromosomal instability'. http://www.ncbi.nlm.nih.gov/pubmed/18192061

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Revision as of 12:11, 4 February 2012

• • IN PROGRESS**

Contents 1 Class Focus, Winter 2012 2 Organizational Meeting: Introduction and Scheduling 2.1 Presentation Zen 2.2 Evaluation Forms 3 Week 1: Tumor Sequencing, part 1 3.1 Papers 3.2 Bonus Materials 3.3 Lecture Slides 4 Week 2: Tumor Sequencing, part 2 4.1 Papers 4.2 Bonus Materials 4.3 Lecture slides 5 Week 3: RNA sequencing 5.1 Papers 5.2 Bonus Materials 6 Week 4: Functional Genomics 6.1 Papers 6.2 Bonus Materials 6.3 Lecture slides 7 Week 5: No Class 8 General Background for Topic 2: Genomic Instability and Cancer 9 Week 6: Chromothripsis 9.1 Papers 9.2 Bonus Materials 9.3 Lecture Slides 10 Week 7: Circadian rhythm and cancer 10.1 Papers 10.2 Bonus Materials 11 Week 8: Inflammation and cancer 11.1 Papers 11.2 Bonus Materials 12 Week 9: TBA 12.1 Papers 12.2 Bonus Materials 13 Week 10: TBA 13.1 Papers 13.2 Bonus Materials 14 Week 11: TBA 14.1 Papers 14.2 Bonus Materials

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]

All Medline abstracts: PubMed HubMed

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]

All Medline abstracts: PubMed HubMed

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: No Class

General Background for Topic 2: 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

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 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

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

Week 9: TBA

Papers

14. = [pmid]

Bonus Materials

Week 10: TBA

Papers

14. = [pmid]

Bonus Materials

Week 11: TBA

Papers

14. = [pmid]

Bonus Materials