Heinrich & Corless Laboratories GIST Research Updates: May 2012

Corless – Will discuss new technologies for DNA sequencing – The goal is to further subclassify GISTs and better understand the genes that contribute to malignancy Heinrich – Will discuss studies aimed at understanding how to kill persistent GIST cells that imatinib and sunitinib cannot always control

‘Next Generation’ DNA Sequencing Traditional DNA sequencing is limited to just one part of one gene at a time Second- and third-generation DNA sequencers are now available at OHSU We have been using these new technologies to study GISTs

Second-Generation DNA Sequencing

Sequencing GIST ‘Exomes’ 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 – this is the ‘exome’ Cost: $2,000 per sample

GIST Exome Sequencing Specimen Summary GenotypeSequencing completedSequencing in progressAvailable PatientsSpecimensPatientsSpecimensPtsSpecimens KIT exon KIT exon PDGFRA3311 Wildtype1133 BRAF13 unknown11 TOTAL Additional matched normal specimens: 19 completed; 5 in progress; 8 available

Sequencing results: Mutant genes by group 25 specimens from 18 patients 285 non-synonymous mutations 276 unique genes Apoptosis, autophagy, 6 Cell adhesion, 5Cell cycle, 1DNA damage response, 4 Epigeneticregulation, 8 GTPase regulation (Ras family), 6 Golgi, intracellular transport, 7 Kinase, adaptor, RTK regulation, 15 Ribosome biogenesis, RNA Polymerase, RNA splicing, 13 Transcription factor, 15 Tumor suppressor, TP53-related, 6 Ubiquitin, 9 Misc potentially interesting, 8 unknown, analysis in progress, 173

GIST Analysis Using Third-Generation DNA Sequencing The Knight Labs have partnered with Ion Torrent/Life Tech on the development of genotyping panels using third- generation DNA sequencing technology Sequencing is performed on a semiconductor chip

Sequencing Directly On A Chip

Traditional Sequence ACTGGTCCTGCTGGTTAG ACTGGTCCAGCTGGTTAG 3 rd Generation Sequence

GIST Panel Knight Diagnostic Labs AKT1PDGFRA AKT2PIK3CA AKT3PTEN ATMPTPN11 BRAFSDHA CDKN2ASDHAF1 HRASSDHAF2 KITSDHB KRASSDHC MAP2K1SDHD NF1TP53 NRAS Important in WT GISTs Common GIST mutations Predicting GIST prognosis Rare GIST mutations of research interest