1. Personalized Therapy of Lung Cancer 2011 Winter Lung Cancer Conference Thomas J. Lynch, Jr., M.D. Jonathan and Richard Sackler Professor of Internal Medicine Director, Yale Cancer Center Physician-in-Chief, Smilow Cancer Hospital

2. Lung Cancer 2011 USA –190,000 cases of lung cancer –165,000 deaths –165,300 cases of NSCLC –115,000 cases of adenocarcinoma –28,500 cases of lung cancer in never smokers Global –1.4 million deaths from lung cancer NCI SEER Cancer Statistics, WHO Fact Sheet.

3. Cancer 2011 Cancer is a disease caused by abnormal genes that “drive” either excessive cell growth or inadequate cell destruction Imbalance of growth and death signals leads to growth of cancer cells into tumors Tumors then proceed to grow and metastasize Understanding which genes drive which cancers will provide a “roadmap” to curing cancer

4. Major Classes of Genomic Alterations that Give Rise to Cancer Point mutations Copy number alterations  Deletions  Amplifications Translocations  Examples: BCR-ABL, EML4, ALK MacConall LE and Garraway LA. J Clin Oncol 2010;28:5219-28.

5. Kate’s Story March 2002: Shortness of breath April 2002: Lung cancer in brain, lung and lymph nodes Summer 2002: Chemotherapy November 2002: Progression in liver

6. Kate November 2002 Pre Rx

7. Kate April 2003

8. Giaccone G et al. J Clin Oncol 2004;22:777-84. Herbst RS et al. J Clin Oncol 2004;22:785-94. INTACT Trials: 1-Year Overall Survival INTACT 1 Gefitinib 500 mg + gemcitabine/cisplatin, 9.9 months Gefitinib 250 mg + gemcitabine/cisplatin, 9.9 months Placebo, 11.1 months INTACT 2 Gefitinib 500 mg + paclitaxel/carboplatin, 8.7 months Gefitinib 250 mg + paclitaxel/carboplatin, 9.8 months Placebo, 9.9 months

9. Sequist LV et al. J Clin Oncol 2008;26(15):2442-9. First-Line Gefitinib in Patients with Advanced NSCLC Harboring Somatic EGFR Mutations Mutations detected in 34/98 patients who underwent direct DNA sequencing of tumor tissue EGFR exons 18 to 21 –In-frame deletions of 11-15 bp, 53% –L858R, 26% –Atypical, 21% Objective response rate, 55% Median progression-free survival, 9.2 months

10. Resistance  There are 2 robustly described TKI-resistance mechanisms: T790M in EGFR and MET amplification  1 patient with both T790M and L858R had a best response of SD and remained on treatment for 55 days Source: Sequist LV et al. Proc ASCO 2007. Abstract 7504

11. T790M Gatekeeper mutation present in nearly 60% of acquired resistance Rare familial germline mutations found Detected at diagnosis in CTCs and circulating DNA in 30% of patients using highly sensitive methods Efforts to target T790M are emerging

12. T790M Irreversible Dual (EGFR, Her-2) kinases have not yet proven effective in this setting Novel T790M specific inhibitor (Nathanael Gray-DFCI) under development Combination therapy might hold best hope

13. Adeno Squam Large Small KRAS Unknown EGFR HER2 BRAF ALK fusion PIK3CA MEK1 ROS fusion PDGFR amp 2011: Lung Adenoca- Multiple Molecular Subsets Courtesy William Pao

14. Adeno Squam Large Small KRAS Unknown EGFR HER2 ALK fusion 2011: Never Smoker Lung Adenoca (US)- Almost All Molecular Subsets Defined! Pham D et al. J Clin Oncol 2006;24(11):1700. Stephens P et al. Nature 2004;431(7008):525. Shaw AT et al. J Clin Oncol 2009;27(26):4247. Riely GJ et al. Clin Cancer Res 2008;14(18):5731.

15. Somatic Mutations Affect Key Pathways in Lung Adenocarcinoma Discovery of more than 1,000 somatic mutations after sequencing 623 genes with known or potential relationships to cancer Identified 26/623 genes that are mutated at a significantly high frequency –Most frequent: TP53, KRAS, STK11, EGFR –Less frequent: LRP1B, KDR, RB1, LTK, SLC38A3, NRAS Genetic alterations frequently occur in genes of the MAPK, p53, Wnt and mTOR pathways Ding L et al. Nature 2008;455:1069-75.

16. McDermott U et al. N Engl J Med 2011;364:340-50.

17. Tumor Tissue Heterogeneity and Microdissection A.H&E micrograph of prostate carcinoma showing epithelial tissue (red arrows) and stroma (black arrow). B.Area of epithelial tissue to be dissected out- lined by etching with laser. C.Tissue section after removal of outlined tissue. D. Removed tissue.

19. EGFR mutation assay on normal tonsil DNA

20. EGFR mutation assay on DNA of a formalin-fixed, paraffin-embedded sample of lung tumor with a heterozygous mutation

21. EGFR G719A, G719S, G719C E746_A750del, E746_S752>V L747_T751, L747_P753>S T790M L858R L861Q KRAS G12S, G12R, G12D, G12V, G12C, G12A G13C, G13S, G13R, G13D Q61K, Q61L, Q61R, Q61H BRAF V600E, V600K NRAS G12C, G12S, G12R, G12D, G12V, G12A G13R, G13C, G13V, G13D, G13A Q61K, Q61L, Q61R, Q61H, Q61P PIK3CA R88Q E542K E545K, E545A, E545G Q546K, Q546R H1047Y, H1047L, H1047R G1049S, G1049R PTEN R130* R173C R233* K267fs* 11 14 17 4 12 2 Gene Mutations tested Cancer type Targeted therapy Total = 60 mutations Lung (26%) TKIs: erlotinib, gefitinib (adenocarcinoma) Lung (17%), colon (15%) Erlotinib, gefitinib; pancreas, biliary tract, cetuximab endometrium, ovary Melanoma (50%), thyroid, PLX4032, biliary tract, colon (12%) GSK2118436 Melanoma (15%), Drugs targeting leukemia, colon (3%) RAS/RAF/MEK pathway Breast, urinary tract, Drugs targeting endometrium, colon (13%), PI3K/AKT/mTOR stomach, melanoma (5%) pathway Endometrium, brain, prostate, colon (10%), melanoma (10-30%)

22. Genome Statistics 29,000 human genes Average gene 3000 bases but wide variation exists 99.9% of our bases are exactly the same from person to person Functions are unknown for 50% of the discovered genes

23. Progress in Sequencing the Human Genome 2000 –12 years –1,800,000,000 USD 2010 –12 days –20,000 USD 2011 –5 days –5,000 USD

24. Yale Genome Statistics Human genome 3.2 billion bases or 3.2 Gbases Sept 2010 Yale sequences 1.8 trillion bases or 1800 Gbases In September Yale sequenced the equivalent of 562 human genomes! In January Yale sequenced 1300 human genomes!

25. Post Genome World 2008 - EGFR and Ras mutation testing routine 2009 - Molecular genotyping - snapshot 2010 - Whole genome sequencing begins experimentally 2012 - Routine WGS available to patients Will we be ready?