Heinrich & Corless Laboratories

GIST Research Updates: May 2011

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

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

‘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

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

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

Sequencing GIST Tumors

Source Status Genotypes Source

OHSU Completed 3 tumors; 1 KIT & 2 PDGFRA D842V Primary

Debiec-

Rychter

Completed 6 tumors; KIT exon 9 or 11; some with

resistance mutations

Primary &

Metastatic

Fletcher Data analysis in

progress

5 tumors; KIT exon 9 with varying

resistance mutations

Metastatic

Bauer Pending 9 tumors; KIT exon 9 or 11; some with

resistance mutations

Primary &

Metastatic

Confirmed Mutations

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

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

Patient Gene AA Change # exons Exon affected Chr

Sequence

confirmed? Gene function

4

BAZ2B S554F 37 9 2q23-q24 pendingbromodomain 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

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

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

GIPC2 L206P 6 4 1p31.1 pending PDZ-containing protein

PRAMEF2 E83K 4 2 1p36.21 pending Nothing known

10(B)KIT INS_AY502-503 21 9 4q11-q12 yes

KIT D816H 21 17 4q11-q12 yes

TP53 G245S 11 7 17p13.1 pending

KIT INS_AY502-503 21 9 4q11-q12 yes

KIT D820E 21 17 4q11-q12 pending

TP53 G245S 11 7 17p13.1 pending

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