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1 Click to edit Master /tle style Tel: (314) Toll Free: (866) Fax: (314) Website: gps.wustl.edu GENETIC TESTING IN CANCER Ka/nka Vigh-Conrad, PhD Genomics and Pathology Services
2 Genomics and Pathology Services (GPS) A lab that offers clinically validated gene/c tes/ng using the latest genomic-level technologies Siteman CCC Genome Ins/tute GPS@WUSTL (Cortex One) WUSM BJC
3 Personalized/Precision medicine Medicine that uses informa/on about a person s genes and environment as part of their clinical care
4 Cancer genelcs Cancer occurs when cells grow uncontrollably due to changes in DNA All cancers have a gene/c component, but not all cancers are hereditary Bad combinalons mutalons cause uncontrolled cell growth Normal cells Tumor cells Inherited (germline) mutalons: passed through genera/ons that puts a person at risk for cancer Found in all cells of the body Tes/ng before gexng cancer to assess risk Only 5-15% of cancers, Ex. BRCA in breast cancer Acquired (somalc) mutalons: happen during person s life/me that ul/mately cause cancer Only in cells of the tumor Tes/ng aqer gexng cancer to personalize management Most cancers, Ex. EGFR in lung cancer
5 Cancer teslng technologies Pathology: CytogeneLcs: Sequencing: Iden/fy morphologic changes to Lssues and cells Iden/fy changes to chromosomes (number, gains, losses, etc.) Iden/fy changes to DNA sequence of genes Single gene tests - common Breast carcinoma histology HER2 posilve breast cancer MulLple gene tests emerging (Next-generaLon sequencing, NGS)
6 Expression-based tests Tests that analyze the expression of a group of genes that can affect how a cancer is likely to behave and respond to treatment
7 Clinical NGS: Why now? Technology improves and costs rapidly decrease Medical knowledgebase expands as we learn more about genomics, pathology, medicine 2005 $10M months to years 1 in 10K Cost Time Error 2014 $4K days to weeks 1 in 100M Manual Highly automated BioinformaLcs for data analysis/management is now available
8 Clinical NGS: workflow & ullity Specimen intake & assessment DNA extraclon DNA sequencing Data analysis & variant annotalon Clinical interpretalon & reporlng Enabling Personalized Medicine Make diagnosis Establish prognosis PATIENT Iden:fy targeted treatment Eliminate unsuitable treatment Iden:fy clinical trial
9 Types of genelc varialon Exon Intron Hotspot GENE Types of genelc varialon Single nucleolde variants (SNVs) C à T Small inserlons/delelons (indels) Inser/on C A Dele/on à C A C A C A à C A (Lost) Structural variants (SV) Transloca/on à Inversion CCTGGTA à ATGGTCC Copy number variants (CNVs)
10 Types of sequencing tests Exon Intron Hotspot GENE Types of sequencing tests Sanger (single locus/gene): muta/on status of one target or a very limited region. Only IDs SNVs and indels. Next-generaLon sequencing (mul/ gene): muta/on status of many genes or regions in one test Amplicon: analysis of specific muta/onal hotspots. Only IDs SNVs and indels Hybrid capture: analysis of en/re coding region. IDs SNVs, indels, some SRs, some CNVs Types of genelc varialon 1. Single nucleo/de variants (SNVs) 2. Small inser/ons/dele/ons (indels) 3. Structural rearrangements (SRs) 4. Copy number variants (CNVs)
11 Types of sequencing tests Exon Intron Hotspot GENE Types of sequencing tests Sanger (single locus/gene): muta/on status of one target or a very limited region. Only IDs SNVs and indels. Next-generaLon sequencing (mul/ gene): muta/on status of many genes or regions in one test Amplicon: analysis of specific muta/onal hotspots. Only IDs SNVs and indels Hybrid capture: analysis of en/re coding region. IDs SNVs, indels, some SRs, some CNVs Types of genelc varialon 1. Single nucleo/de variants (SNVs) 2. Small inser/ons/dele/ons (indels) 3. Structural rearrangements (SRs) 4. Copy number variants (CNVs)
12 Types of sequencing tests Exon Intron Hotspot GENE Types of sequencing tests Sanger (single locus/gene): muta/on status of one target or a very limited region. Only IDs SNVs and indels. Next-generaLon sequencing (mul/ gene): muta/on status of many genes or regions in one test Amplicon: analysis of specific muta/onal hotspots. Only IDs SNVs and indels Hybrid capture: analysis of en/re coding region. IDs SNVs, indels, some SRs, some CNVs Types of genelc varialon 1. Single nucleo/de variants (SNVs) 2. Small inser/ons/dele/ons (indels) 3. Structural rearrangements (SRs) 4. Copy number variants (CNVs)
13 Comprehensive Cancer Gene Set SomaLc variant analysis of tumors Hematologic Malignancies ABL1 ASXL1 CEBPA DNMT3A FLT3 JAK2 KTM2A MPL MYC MYD88 NOTCH1 NPM1 PTPN11 RUNX1 TET2 BRAF IDH1 IDH2 KIT TP53 PDGFRA Solid Tumors AKT1 ALK APC ATM BRCA1 BRCA2 CDKN2A CTNNB1 EGFR FGFR2 ERBB2 ESR1 HRAS KRAS MAP2K2 MET MTOR NF1 NRAS PIK3CA PTCH1 PTEN RB1 RET SMO STK11 VHL WT1 Covers aclonable genes and variants those that aid in diagnosis, prognosis, and the selec/on of therapies to guide treatment decisions Highly sensilve detec/on of muta/ons from archival specimens Concise interpretalons of genomic findings 49 genes total Cost-effecLve and high success of reimbursement
14 Updated tests April 2015 Ø Solid Tumor Gene Set (48 genes) AKT1, AKT2, AKT3, ALK*, ATM, BAP1, BRAF, BRCA1, BRCA2, CDH1, CDKN2A, CTNNB1, EGFR, ERBB2, ESR1, FGFR1, FGFR2*, FGFR3*, FLT3, GNAS, HRAS, IDH1, IDH2, JAK1, JAK2, KIT, KRAS, MAP2K1, MAP2K2, MET, MLH1, MTOR, MYC, NF1, NOTCH1, NRAS, NTRK1*, PDGFRA, PDGFRB, PIK3CA, PTEN, RB1, RET*, RIT1, ROS1*, STK11, TP53, VHL Breast cancer genes AKT1, BRCA1, BRCA2, CDH1, ERBB2, FGFR1, FGFR2*, PIK3CA, PTEN, STK11, TP53 Ø HematopoieLc Disorders Gene Set (43 genes) ABL1, ASXL1, ATM, BCOR, BIRC3, BRAF, CALR, CBL, CEBPA, CSF3R, DNMT3A, EP300, ETV6, EZH2, FBXW7, FLT3, GATA1, IDH1, IDH2, IKZF1, JAK2, KIT, KRAS, KNT2A*, MPL, NF1, NOTCH1, NPM1, NRAS, NSD1, PDGFRA, PDGFRB, PTPN11, RUNX1, SETB1, SF3B1, SRSF2, STAG2, TET1, TET2, TP53, U2AF1, ZRSR2 * Selected introns also sequenced for rearrangement detection
15 CLINICAL ullity: Who is the right palent? In early-stage disease Common Lung Skin AML DiagnosLc info PrognosLc info Targeted therapies Kinase inhibitors (Kis) Monoclonal an/bodies (mabs) Emerging Breast Brain Colorectal In relapse, refractory or advanced stage disease Limited Lymphoma Pancreas Prostate Pan cancer: Off-label drug therapies Clinical (basket) trial enrollment
16 Genes are not so far ahead of drugs Breast cancer: 73 medicines in development 2004: nine monoclonal an/bodies and ~12 inhibitors 2014: 91 FDAapproved targeted cancer therapies 2014: 771 agents in U.S. Clinical Trials or awai/ng FDA review Medicines in Development Cancer 2014 hjp://
17 EXPERIENCE: >2000 tests Breakdown by cancer type DistribuLon of aclonable variants Hematologic 5% GYN 5% Pancreas 6% Sarcoma 7% Brain 4% GI 8% Other 3% Head & neck 11% Lung 35% Colorectal 14% Breast 2% Level 1 Ac/onable in tumor type Level 2 Ac/onable in another tumor type Level 3 Reported in cancer / other disease VUS or SNP 47% Level 1 16% Level 3 23% Level 2 14%
18 Breast cancer epidemiology 200,000 breast cancer diagnoses per year in US 5-10% associated with hereditary predisposilon BRCA1/2 muta/on posi/ve risks Breast cancer (life/me risk): ~65-80% Ovarian cancer : ~40% for BRCA1; ~12-20% for BRCA2 Male breast cancer: 1-10% Prostate cancer: up to 39% Pancrea/c cancer: 1-7%
19 GeneLcs of breast cancer Germline mutalons SomaLc mutalons Gene Syndrome RelaLve risk of BC BRCA1 BRCA2 Hereditary breast & ovarian cancer Hereditary breast & ovarian cancer Major associated cancer Ovarian, pancrea/c Ovarian, prostate, pancrea/c p53 Li-Fraumeni Sarcoma, brain, adrenocor/cal, leukemia, colon PTEN Cowden s, Bannayan- Riley-Ruvalcaba 2-4 Thyroid, endometrial, genitourinary STK11 Peutz-Jeghers 15 Small-intes/ne, colorectal, uterine, tes/cular, ovarian CDH1 Hereditary diffuse gastric carcinoma 3.25 Diffuse gastric Gene BRCA1 BRCA2 AKT1 FGFR1 FGFR2 ERBB2 (HER2) PIK3CA PTEN
20 ULlity of genelc teslng in BC Germline: asses risk, prognosis Early screening for early detec/on Preventa/ve measures (masectomy, oophorectomy ) SomaLc: therapeu/c op/ons, prognosis BRCA1/2: More sensi/vity to chemotherapy with PARP inhibitors FGFR1/2: Sensi/vity to kinase inhibitors ERBB2 (HER2): Sensi/vity to Hercep/n PIK3CA/PTEN: trials for single vs. combina/on therapies Many inhibitors in clinical development or trial stage - PI3K/AKT, PARP, ERBB2(HER2), MET, ESR1
21 Thank you! Q&A with Dr. Jon Heusel Chief Medical Officer of GPS Associate Professor in Pathology & Immunology
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