Heinrich & Corless Laboratories GIST Research Updates: May 2011

1. Heinrich & Corless Laboratories GIST Research Updates: May 2011

2. Genotyping for Clinical Trials • Regorafenib (Bayer) – phase II trial • Tyrosine kinase inhibitor • 3rd/4th line therapy for resistant GISTs • Initial results will be reported at ASCO • FDA has put the drug on fast-track for review • Phase III trial is getting underway • Synta • HSP90 inhibitor (intravenous) • Phase II trial ongoing

3. Genotyping for Clinical Trials • PERSIST trial • Ron DeMatteo’s trial of 5 years of adjuvant imatinib • More than 50% enrolled • ImClone • Antibody against PDGFRA • Phase II trial for KIT-mutant or PDGFRA-mutant tumors resistant to imatinib & sunitinib • Phase I/II trial for a new drug that Mike will talk about

4. ‘Next Generation’ DNA Sequencing • Traditional DNA sequencing is limited to just one part of one gene at a time • Second-generation DNA sequencers are now available and have begun to revolutionize cancer research by generating information on thousands of genes simultaneously • Starting last summer, we have been using this new technology to study GISTs

7. Sequencing Data • Human genome consists of 3.2 billion letters (A, C, T, G) • Genes comprise only ~2% of our DNA (about 64 million letters) • We ‘pre-select’ the genes, so that only the 64 million letters of interest get sequenced • Cost: $3,000 per sample

8. Sequencing Data • First experiment: 8/2010 • Illumina GAIIX ~1,000,000,000 letters per experiment • Most recent experiment: 4/2011 • Illumina HiSeq ~10,000,000,000 letters per experiment

9. Sequencing GIST Tumors

10. Patient Gene AA Change # exons Exon affected Chr Sequence confirmed? 1 PDGFRA D842V 23 18 4q11-q13 yes HNRNPA2B1 S36G 12 3 7p15 yes 2 PDGFRA D842V 23 18 4q11-q13 yes TP53 C135G 11 5 17p13.1 yes MDN1 E661K 102 14 6q15 yes KEL T421M 19 11 7q33 yes TACR3 S435N 5 5 4q25 yes CTNND2 N1211S 21 21 5p15.2 yes INSR S995A 22 16 19p13.3-p13.2 yes 3 KIT V559D 21 11 4q11-q12 yes LAS1L Q634L 14 12 Xq12-q13 yes ODZ1 R1519C 31 24 Xq25 yes TP53 L348S 11 10 17p13.1 yes COL1A2 G430E 52 23 7q22.1 yes TP53 G245C 11 7 17p13.1 yes DDEF1/ASAP1 W18C 29 1 8q24.1-q24.2 yes SAT1 H53Q 3 3 Xp22.1 yes Confirmed Mutations

11. Patient Gene AA Change # exons Exon affected Chr Sequence confirmed? Gene function 4 BAZ2B S554F 37 9 2q23-q24 pending bromodomain adjacent to zinc finger domain FAM134A V296M 9 8 2q35 pending Possible relationship with lung ca metastasis? TNFRSF11B I312T 5 5 8q24 pending osteoblast-secreted decoy receptor that functions as a negative regulator of bone resorption. This protein specifically binds to its ligand, osteoprotegerin ligand SERINC2 T245N 10 6 1p35.1 pending Nothing known SHBG A210V 8 5 17p13-p12 pending Steroid binding globulin C10orf82 L149M 4 5 10q25.3 pending Nothing known IFNGR1 N433Y 7 7 6q23-q24 pending interferon gamma receptor 1 PCDHB16 P390H 1 1 5q31 pending Ca++ Cell adhesion 7(A) KIT D816G  21  17 4q11-q12 yes LASS2 L45M 11   2 1q21.2 pending Growth regulation; sphingolipid synthesis FAM176A V12M  4  3 2p12 pending Apoptosis/autophagy AAAS A167T  16 6  12q13 pending COL1A2 A683D 52  34  7q22.1 pending 7(B) KIT Y823D  21  17 4q11-q12 yes LASS2 L45M 11  2  12q13 pending Growth regulation; sphingolipid synthesis FAM176A V12M  4  3 2p12 pending Apoptosis/autophagy 8 GIPC2 L206P 6  4  1p31.1 pending PDZ-containing protein PRAMEF2 E83K 4  2  1p36.21 pending Nothing known 10(A) KIT INS_AY502-503  21  9  4q11-q12 yes KIT D816H  21  17  4q11-q12 yes TP53 G245S 11 7 17p13.1 pending 10(B) KIT INS_AY502-503  21  9  4q11-q12 yes KIT D820E  21  17  4q11-q12 pending TP53 G245S 11 7 17p13.1 pending

12. Knight Diagnostic Laboratories • The Corless laboratory has recently been integrated into the new Knight Diagnostic Laboratories • These Labs are now operating independent from OHSU Hospital • Mandate from Dr. Druker: • Offer the most advanced genotyping in the country • Expand outreach to serve as many cancer patients as possible