The Many Faces of Personalized Health Care: Pediatric and Medical Oncology Joshua D. Schiffman, MD Edward B. Clark, MD Chair in Pediatric Research Associate Professor, Pediatric Hematology/Oncology University of Utah School of Medicine April 01, 2014

The Cancer Challenge Second leading cause of death worldwide 8 million deaths per year worldwide 15 people die from cancer every minute 1/2 of all men and 1/3 of all women will get cancer Relapse is leading cause of cancer-related death

Huntsman Cancer InstituteARUP Laboratories Translational Oncology Core Pilot Study

Translational Oncology Core Pilot Study Enroll RELAPSED cancer patients (N=200) Pre- and post-test survey to clinician Sequenom Panel (OncoCarta Custom) – 277 mutation in 25 genes – Return report to clinician OncoScan Array V3.0 (N=48) – Genome-wide Copy Number/LOH – 74 Mutations in 9 Genes

Translational Oncology Core Pilot Study Sequenom: – ABL1, AKT1, AKT2, BRAF, CDK4, CTNNB1, EGFR, ERBB2, FGFR1, FGFR3, FLT3, HRAS, JAK2, JAK3, KIT, KRAS, MET, MYC, NRAS, PDGFRA, PIK3CA, PTEN, RB1, RET, VHL OncoScan (Affy): – BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS, TP53

…So what did we find?

Huntsman Cancer Institute: Molecular Diagnostic/Translational Oncology Core (TOC) Pilot Study Positive Mutation Frequency 48 out of 137 specimens were positive for ≥1 mutation (35%)

Huntsman Cancer Institute: Molecular Diagnostic/Translational Oncology Core (TOC) Pilot Study Tumor Types Analyzed by OncoScan (N=48) 15 ovarian/endometrial 15 colorectal tumors 12 melanoma 4 lung tumor 1 brain tumor 1 thyroid tumor Tumor Types Analyzed by OncoScan (N=48) 15 ovarian/endometrial 15 colorectal tumors 12 melanoma 4 lung tumor 1 brain tumor 1 thyroid tumor

Clinically actionable/relevant copy number genes (N=100) ABL1, AKT1, AKT2, ALK, APC, AR, ARID1A, ASXL1, ATM, AURKA, BAP, BAP1, BCL2L11, BCR, BRAF, BRCA1, BRCA2, CCND1, CCND2, CCND3, CCNE1, CDH1, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CEBPA, CTNNB1, DDR2, DNMT3A, E2F3, EGFR, EML4, EPHB2, ERBB2, ERBB3, ESR1, EWSR1, FBXW7, FGF4, FGFR1, FGFR2, FGFR3, FLT3, FRS2, HIF1A, HRAS, IDH1, IDH2, IGF1R, JAK2, KDM6A, KDR, KIF5B, KIT, KRAS, LRP1B, MAP2K1, MAP2k4, MCL1, MDM2, MDM4, MET, MGMT, MLL, MPL, MSH6, MTOR, MYC, NF1, NF2, NKX2-1, NOTCH1, NPM, NRAS, PDGFRA, PIK3CA, PIK3R1, PML, PTEN, PTPRD, RARA, RB1, RET, RICTOR, ROS1, RPTOR, RUNX1, SMAD4, SMARCA4, SOX2, STK11, TET2, TP53, TSC1, TSC2, VHL Ciriello et al., Nat Genet. (2013) / Frampton et al., Nat Biotechnol. (2013) Pritchard et al., J Mol Diagn. (2014) / Andre et al., Lancet Oncol. (2014)

TOC Colorectal Adenocarcinoma OncoScan Results (N=15) Genome view (Nexus, BioDiscovery, Inc.)

Copy number aberrations in 15 colorectal adenocarcinoma cases

BMP-039 Metastatic tumor (left ovary) 90% tumor content by Sequenom KRAS G12S mutation

BMP-039 Metastatic tumor (left ovary) 90% tumor content by Sequenom KRAS G12S mutation

Focal CCND1 gain (4 copies) in LOH region in case BMP-18 Metastatic CRC (liver and bile duct) 50% tumor content by Sequenom KRAS G12D mutation Metastatic CRC (liver and bile duct) 50% tumor content by Sequenom KRAS G12D mutation

Focal CDK6 gain (7 copies) in BMP-46 Metastatic CRC (right colon) 30% tumor content by Sequenom KRAS G12C mutation Metastatic CRC (right colon) 30% tumor content by Sequenom KRAS G12C mutation

Next Study Design: 360 Degree Profiling Mutation Panel Genome-wide copy number Genome-wide transcriptome Genome-wide methylation 360 Degree Profiling Mutation Panel Genome-wide copy number Genome-wide transcriptome Genome-wide methylation Relapsed Pediatric Tumors Relapsed Colorectal Cancer Relapsed Ovarian/Endometrial Relapsed Melanoma Relapsed Sarcoma

Utah and Pediatric Cancer

Tumors found by early screening (Utah) 9 yo boy (TP53) 17 yo girl (TP53) 24 yo man (TP53) 41 yo woman (TP53) 30 yo man (SDHB) 51 yo woman (SDHB) 58 yo man (SDHB) 34 yo man (SDHB) Grade II Glioma Grade III AA Lung Adenoca. Renal Cell Carcinoma Carotid Body Tumor Pheochromocytoma

Villani et al. Lancet Oncology (2011) 100% Survival! P= LFS families −33 TP53 mut + −18 surveillance −12 no surveillance Surveillance − 10 tumors, 7 pts − All pts alive No Surveillance − 12 tumors, 10 pts − 2 alive (20%) Screening TP53 mutation carriers 20% Survival

Bella Johnson, Anne Naumer, Wendy Kohlmann Cancer Genetics Study (CGS) Familial cancer syndrome global registry and biospecimen bank Enroll children and families at high risk for cancer DNA, cell lines, and tumor samples Biology and clinical data linked to family pedigrees Participants linked to UPDB

Cancer Genetics Study Data collection – Cancer history – Medical history – Genetic testing – Cancer screening – Patient reported family history – Linked to UPDB genealogy records Databases – CCR, Subject, itBioPath, Progeny

Sample collection – 1ACD tube for cell lines (limited availability) – 1 EDTA tube for DNA and plasma – 1 Red top tube for serum – 1 PAXgene tube for RNA – 1 CPT tube for PBMC – Archived tissue or excess tissue from surgery if not already in TRAC Cancer Genetics Study

PCH Pediatric Cancer Program Life Course Health Care Complications and Costs – Anne Kirchhoff, PhD Value-Based Pediatric Clinical Cancer Care – Richard Lemons, MD PhD Advanced Therapeutic Approaches to Pediatric Cancer – Mike Spigarelli, MD PhD Identifying New Genes and Novel Screening Approaches for Pediatric Cancer – Joshua Schiffman, MD

DICER1 Family “I’m not sure that you guys are really going to be able to find anything with this study if you are stupid enough to drive out here in this weather.”

1.Precision Oncology is happening now at University of Utah 2.Early tumor surveillance in patients at genetic risk for cancer saves lives 3.PCH Pediatric Cancer Program identifying late effects, toxicities, pharmaco- dynamics, and genetic risks 4.UGP is finding cancer-associated genes Summary

Questions?

Schiffman Lab –Lisa Abegglen –Christin Christensen –Ashley Chan –Marcus Stucki –Jamie Gardiner –Tonya Santoro –Kristy Lee –Sharanya Raghunath –Clint Mason ARUP –Sarah South, Xinjie Xu, Erica Andersen, Reha Toydemir Nexus (BioDiscovery) –Soheil Shams, PhD RESEARCH SUPPORT: ASH Scholar Fellowship Award Curesearch Foundation (Children’s Oncology Group) St. Baldrick’s Foundation Alex’s Lemonade Stand Foundation SARC Career Development Award Children’s Health Research Career Development Award (5K12HD ) Damon Runyon Clinical Investigator Award Leukemia & Lymphoma Society 1R01CA (NCI/NIH)

Colorectal Cancer Mutation Summary Sample IDCNA/LOHSequenomOncoScan BMP No mutations BMP-006+KRAS G12DKRAS G12D (6.59) BMP-015+BRAF V600EBRAF V600E (9.31) BMP KRAS G12C PIK3CA E542K KRAS G12D/V (8.83) PIK3CA E542K (41.22) BMP-018++KRAS G12DKRAS G12D/V (10.21) BMP KRAS G12DKRAS G12D/V (12.44) BMP-025++No mutations BMP-033++No mutations BMP-036+KRAS G12VKRAS G12D/V (11.36) BMP-039++KRAS G12SKRAS G12C/S (46.16) BMP-040++KRAS G12DKRAS G12D/V (12.47) BMP No mutations BMP-043- PTEN K267fs*9 PIK3CA C420R BRAF V600E PTEN K267fs*9 (128.56) (not included in panel) BRAF V600E (57.54) BMP-046++KRAS G12CKRAS G12C/S (21.45) BMP-047++JAK3 V7221(not included in panel) 14/15 (93%) = Copy Number Present 8/15 (53%) = KRAS mutations 2/15 (13%) = PIK3CA mutations 2/15 (13%) = BRAF mutations 1/15 (7%) = JAK3 mutation

SampleCNASequenomOncoScan BMP 1 YesNo Mutations BMP 4 YesPIK3CA p.E545K BMP 5 YesNo Mutations BMP 8 YesNo Mutations TP53 p.R273H/L BMP12 YesNo Mutations BMP20 YesPIK3CA p.R88Q TP53 p.R248Q/L BMP23 YesNo Mutations BMP26 YesPTEN p.N323fs*2 KRAS p.G12D/V (Score:8.32) BMP27 YesNo Mutations BMP28 Yes PIK3CA p.H1047R PTEN p.R130G PIK3CA p.H1047R PTEN p.R130G BMP29 NoNo Mutations BMP42 YesNo Mutations BMP44 YesPIK3CA p.Q546K BMP45 YesNo Mutations BMP48 YesNo Mutations Ovarian and Endometrial Samples (N=15): Mutation Summary 14/15 (93%) = Copy Number Present 4/15 (27%) = PIK3CA mutations 2/15 (13%) = PTEN mutations 2/15 (13%) = TP53 mutations

Metastatic Melanoma (N=12): Mutation Summary Case IDCNAsBy SequenomBy OncoScan BMP-009 Yes NRAS Q61K Mutation BMP-010 Yes No Mutations BMP-013 Yes NRAS G12C Mutation BMP-014 Yes BRAF V600E Mutation BMP-019 Yes No Mutations BMP-021 Yes NRAS Q61R mutation BMP-024 Yes No Mutations BMP-030 Yes PIK3CA H701P mutationNo Mutations BMP-031 Yes NRAS Q61K Mutation BMP-034 Yes BRAF K601E MutationNo Mutations BMP-035 Yes PTEN R130fs*4 mutation BMP-037 Yes No Mutations(CCND1 amplification) 12/12 (100%) = Copy Number Present 4/12 (33%) = NRAS mutations 2/12 (17%) = BRAF mutations 1/12 (8%) = PTEN mutation 1/12 (8%) = PIK3CA mutation