Valida5on of a Microsatellite Instability Assay by NGS

Transcription

1 Valida5on of a Microsatellite Instability Assay by NGS Mark R. Miglarese, Ph.D. VP R&D 1

2 Caris Life Sciences 230,000+ tests performed in 2016 Headquarters: Irving, Texas Laboratory: Phoenix, Arizona 66,000 sq. O. oncology- focused ISO 15189, CLIA, CAP, NY State and CE Mark approved/cer5fied Profiled 120,000+ pa9ents 7,000+ physicians All 50 states 63 countries Laboratory staff Pathologists Molecular Gene5cists Consul5ng Medical Oncologists MD and/or PhD literature evidence review team ~100 trained molecular & laboratory technicians 2

3 Comprehensive Technological Arsenal Fuels Inven5on Across a Broad Range of Molecular Biology Comprehensive Technology Suite Sequencing (Next- Gen, Whole Exome, Sanger, Pyro) Nanostring PCR (ddpcr, nanoliter scale PCR, qpcr, RT- PCR) Laser Capture Microdissec5on In Situ Hybridiza5on Histology, special stains Immunohistochemistry Autostaining (DAKO, Ventana) Slide imaging Immunoprecipita5on, immunoblohng Cell culture ELISA Robo5cs Protein cross- linking Microarray Mass Spec (Maldi TOF, Quan5ta5ve proteomics) HPLC, FPLC Polyligandhistochemistry Luminex Surface plasmon resonance Dynamic Light Scajering Fluorescent Ac5vated Cell Sor5ng In vitro pharmacology Oligo synthesis (na5ve or modified) Nanosight Exosome isola5on and characteriza5on Liposomal formula5ons Mul9- Disciplinary Exper9se Bioinforma5cians Mathema5cians/Sta5s5cians Medical Oncologists Molecular Biologists Molecular Gene5cists Molecular Pathologists Research Scien5sts 3

4 Caris Clinical Tes5ng Menu Next Gen DNA Sequencing Illumina NextSeq System ü 592 full genes sequenced ü Includes all SNVs and indels on guidelines ü Includes nearly all markers included in clinical trials Also reported Ø Total Muta5onal Load Ø Copy Number Varia5on on 442 genes Ø Micro Satellite Instability Next Gen RNA Sequencing Illumina MiSeq System ü 53 genes sequenced ü Novel transloca5on detec5on independent of intronic breakpoint ü ALK transloca5on ü ROS1 transloca5on ü RET transloca5on ü NTRK 1-3 transloca5ons ü CMET exon 14 skipping ü EFGFv3 ü BRAF transloca5on ü RSPO3 transloca5on Protein Expression Ventana & Dako Immunohistochemistry ü 25 lineage specific IHC ü Lung ü PDL- 1 (22c3) ü ALK ü PTEN ü RRM1 ü TOPO1 ü TS ü TUBB3 ü CRC ü MMR markers ü Breast ü ER, PR, AR, Her2 hjp:// profiling- menu/individual- tumor- profiling- menu- usa/ 4

5 Iden5fying key molecular features that bring value requires understanding the complexity of the system we are working within Low Complexity & Func9onal Diversity High 5

6 Caris CMI Testing for Immunotherapies 6

7 The World just Changed FDA approved pembro across all solid tumors that are MSI- High 7

8 MSI leads to an increase in the number of neoan5gens and increases the likelihood of immune recogni5on Nature Biotechnology 8

9 Responses observed in a large propor5on of pa5ents (Le et al. Science 2017) 9

10 Significant increase in survival was observed across MSI- High pa5ents (Le et al. Science 2017) 10

11 Tradi5onal approach employs PCR to compare tumor to normal across 5 loci 11

12 Distribu5on of 27,039 polymorphic microsatellite markers across the human genome Tamiya (2005). Human molecular gene5cs /hmg/ddi

13 MSI Valida5on Process Compare NGS data to PCR (comparing cancer and normal 5ssue) on ~2200 pa5ents Algorithm Training: Maximize Sensi5vity, Specificity, NPV, and PPV Test on 200 Naïve pa5ents and compare to MSI by PCR and MMR by IHC All (2196 Pa9ents) Sensi5vity Specificity PPV NPV 95.8% 99.4% 94.5% 99.2% CRC (1198 Pa9ents) Sensi5vity Specificity PPV NPV 100.0% 99.9% 98.7% 99.6% 13

14 Distribu5on of in- dels across 5K pa5ents MSI Frequency of patients Number of loci 14

15

16 NGS MSI Count per Sample Uveal Melanoma Thyroid Carcinoma Thymic Carcinoma Soft Tissue Tumors Small Intestinal Malignancies Retroperitoneal or Peritoneal Sarcoma Retroperitoneal or Peritoneal Carcinoma Prostatic Adenocarcinoma Pancreatic Adenocarcinoma Ovarian Surface Epithelial Carcinomas None Of These Apply Non Epithelial Ovarian Cancer (non EOC) Nodal Diffuse Large B Cell Lymphoma Neuroendocrine tumors Multiple Myeloma Melanoma Malignant Solitary Fibrous Tumor of the Pleura (MSFT) Male Genital Tract Malignancy Lymphoma Lung Small Cell Cancer (SCLC) Lung Non small cell lung cancer (NSCLC) Lung Bronchioloalveolar carcinoma (BAC) Low Grade Glioma Liver Hepatocellular Carcinoma Kidney Cancer Head and neck Squamous Carcinoma Glioblastoma Gastrointestinal Stromal Tumors (GIST) Gastric Adenocarcinoma Female Genital Tract Malignancy Extrahepatic Bile Duct Adenocarcinoma Esophageal and Esophagogastric Junction Carcinoma Colorectal Adenocarcinoma Cholangiocarcinoma Breast Carcinoma Bladder Cancer Acute myeloid leukemia (AML)

17 Rela5onship between MSI, TML, PDL- 1 All Lineages 8.1% of Pa5ents are TML high TML MSI N=8952 3% of Pa5ents are MSI unstable % of Pa5ents are PDL- 1 posi5ve PDL1 17

18 MSI is highly correlated to TML in Colorectal Cancer Pa5ents 18

19 MSI- NGS vs. TML rela5onship depends on lineage 19

20 Rela5onship of other immunotherapy markers to MSI- NGS 20

21 Frequency of MSI across lineages Stage 4 Stage 3 (Le et al. Science 2017) 21

22 Thank you! 22