NGS IN ONCOLOGY: FDA S PERSPECTIVE ASQ Biomed/Biotech SIG Event April 26, 2018 Gaithersburg, MD You Li, Ph.D. Division of Molecular Genetics and Pathology Food and Drug Administration (FDA) Center for Devices and Radiological Health (CDRH) Office of In Vitro Diagnostics and Radiological Health (OIR) 1
Disclaimer The views expressed during this presentation are preliminary and do not necessarily reflect the final policy or position of the US FDA or the US government. 2
What is NGS Oncopanel? Overview Regulatory Paradigm for NGS oncopanel Validation Strategy (MSK-IMPACT case study) Resources (facilitate NGS oncopanel development) 3
www.genome.org 4
NGS Revolutionized Personalized Genomics & Medicine NGS is the driving technology for precision medicine. NGS assays have been widely adopted to clinical use. 5 5
www.genome.org 6
What is NGS Oncology Panel? A NGS based tumor test, which enables systematic interrogation of numerous biomarkers from a predefined cancer-related genes from a patient s tumor specimen. NGS oncopanels are increasingly employed for clinical use. 7 7
FDA NGS Oncopanel Review Paradigm Level-1 CDx Level-2 Cancer mutations with evidence of clinical significance Level-3 Cancer mutations with potential clinical significance 8
Oncomine Dx Target Test lung cancer panel (June 22, 2017) Qualitative in vitro diagnostic test that uses targeted high throughput, parallel-sequencing technology to detect single nucleotide variants (SNVs) and deletions in 23 genes from DNA and fusions in ROS1 from RNA isolated from formalin- fixed, paraffinembedded (FFPE) tumor tissue samples from patients with nonsmall cell lung cancer (NSCLC) using the Ion PGM Dx System. Gene Variant Targeted therapy BRAF BRAF V600E TAFINLAR (dabrafenib) in combination with MEKINIST (trametinib) ROS1 ROS1 fusions XALKORI (crizotinib) EGFR L858R, Exon 19deletions IRESSA (gefitinib) 9
Tumor Profiling NGS tests Review Paradigm Level-1 Level-2 CDx Cancer mutations with evidence of clinical significance Class II path for NGS tumor profiling tests Level-2 biomarkers: Clinical validity established in professional guidelines, but NOT demonstrated with the test. Level-3 Cancer mutations with potential clinical significance Level-3 biomarkers: Clinical validity not demonstrated either in professional guidelines or with the test, but suggestive based on clinical/biological evidence. 10
MSK-IMPACT (Nov 15, 2017) De novo authorization of MSK-IMPACT assay established a new class II regulatory pathway for NGS-based tumor profiling tests. This designation makes these tests eligible for the 510(k) clearance process, either by applying to the FDA directly or through an accredited third-party reviewer like NYSDOH. 11
FoundationOne CDx (F1CDx) (November 30, 2017) Broad-panel follow-on companion diagnostic test for 5 tumor indications Genomic profiling of 324 genes, MSI & TMB in all solid tumors Breakthrough Parallel Review www.fda.gov 12
F1CDx Approved CDx Indications 13
NGS Tumor Profiling Assay FDA authorized the first NGS Tumor Profiling Oncopanel (MSK-IMPACT) on November 15, 2017. The De Novo authorization established a new class II regulatory pathway for NGS tumor profiling tests. Future NGS tumor profiling tests are eligible for 510(k) clearance process, either by applying directly to FDA or through an accredited third-party reviewer (such as NYSDOH). What documents and validation data are needed in a NGS tumor profiling 510(k) submission? 14
MSK-IMPACT Tumor Profiling Assay Review Elements Intended Use Statement Device Description Analytical Validation Pre-analytical Analytical Studies Clinical Validation Instrument/Software Labeling Post-market modification protocols 15
MSK-IMPACT Intended Use The MSK-IMPACT assay is a qualitative in vitro diagnostic test that uses targeted next generation sequencing of formalin-fixed paraffin-embedded tumor tissue matched with normal specimens from patients with solid malignant neoplasms to detect tumor gene alterations in a broad multi gene panel. The test is intended to provide information on somatic mutations (point mutations and small insertions and deletions) and microsatellite instability for use by qualified health care professionals in accordance with professional guidelines, and is not conclusive or prescriptive for labeled use of any specific therapeutic product. MSK-IMPACT is a single-site assay performed at Memorial Sloan Kettering Cancer Center. 16
Device Description Assay Configuration: NGS-based hybrid capture oncology panel (468 genes, 6000+ exons) Tumor/matched normal paired sequencing (minimize errors and detect true somatic mutations) Reportable Range: SNVs/MNVs, small indels from 468 genes (73 exons excluded), MSI-status QC and Optimization: External positive/negative controls included for each run Extensive QC measures for each assay step Quality metrics thresholds (at run, sample, exon and variant level) optimized to improve assay performance Variant Reporting: Use MSK curated public database OncoKB for clinical interpretation. Report variants under two categories (based on levels of clinical evidence) 17
Analytical Performance Accuracy (concordance to orthogonal testing) Limit of Detection (detection sensitivity) Precision (repeatability and reproducibility) Real-World Evidence: historical data across different tumor types to support pan-tumor claim. (MSK Nat Medicine manuscript, April 2017) *Additional analytical performance studies to support CDx claim: interference, stability, robustness, etc. 18
Analytical Accuracy Tested 433 FFPE samples across different cancer types. Samples cover clinically significant ( actionable ) mutations from 20 genes (48 exons). 267 unique variants assessed cover different variant types (SNV, MNV, insertions, deletions). Accuracy were demonstrated for both positive and negative (wildtype) calls. 19
LoD and Precision LoD Establishment: Dilution study to estimate LoD for each variant type. LoD Confirmation: Precision using clinical specimens at the LoD level. Precision (sample selection): Clinical FFPE specimens from different tumor types, selected based on presence of clinically significant mutations across different variant types. Precision (panel-wide analysis) - In addition to known mutations, precision analysis was performed for all incidental somatic mutations (82 total) identified from replicate testing. - Precision analysis not only on variant call agreement, but also on key quality metrics (coverage, VAF, normalized coverage etc.) 20
MSI Validation MSI status determined by tumor/matched normal comparison of 1000+ microsatellite loci using MSIsensor algorithm. MSIsensor score (% unstable loci) >=10 is used to define MSI-H. (Different MSI-H definition from clinical practice guidelines, clearly stated in the test report) Cutoff established using 201 colorectal and endometrial carcinoma (CRC/EC) cases (training dataset). Independently validated by concordance to PCR-MSI or IHC-dMMR results from both CRC/EC and Non- CRC/Non-EC cohorts. MSI LoD and precision were assessed. Supplemental data from MSK s recent publication (>12,000 patient cohort) to support pan-tumor MSI validation. 21
Clinical Validation for Tumor Profiling Claim Gene inclusion rationale (cancer relevance) Mutation prevalence across tumor types (leverage MSK publication) Curation rules for evidence of clinical significance (OncoKB) Variant reporting (classification criteria, limitation statements) 22
Test Report Use OncoKB database for clinical evidence curation. Report variants under two categories, based on cancer-specific levels of clinical evidence. - Cancer Mutations with Evidence of Clinical Significance - Cancer Mutations of Potential Clinical Significance Transparent test limitation statements. 23
NGS Oncopanels: Tumor Profiling vs. CDx Difference between NGS CDx and Tumor Profiling Assays CDx Tumor Profiling IU Conclusive/Prescriptive use for specific therapeutics? Yes (IU specifies CDx biomarker and approved drug indications) No Clinical Clinical validity (for selecting treatment) established using the test? Yes (clinical efficacy or clinical concordance) No Analytical Variant level validation data provided? Yes (for each CDx biomarker) Not always Regulatory Pathway Currently eligible for 510(k) clearance? No (PMA) Yes 24
Third Party Review Program FDA accredited NYS Department of Health as the first 3 rd party reviewer for NGS tumor profiling assay. NGS tumor profiling 510(k) can be submitted directly to FDA or through NYSDOH Review elements and requirements are identical in both pathways. Special controls established in MSK-IMPACT De Novo must be met in order to obtain 510(k) clearance. 25
Conclusion NGS oncopanels allows simultaneous evaluation of multiple genetic biomarkers from different genes from a tumor specimen. The tumor genomic profiling is critical for treatment and management of cancer patients. Two regulatory pathways available for NGS oncopanels. - NGS CDx and NGS tumor profiling test Analytical and clinical validation are needed to demonstrate safe & effective use of the test. 26
Resources CDRH Pre-Submission Program: https://www.fda.gov/downloads/medicaldevices/deviceregulationandguidanc e/guidancedocuments/ucm311176.pdf Questions? You.Li@fda.hhs.gov CDRH FACT SHEET - Tumor Profiling NGS Tests: https://www.fda.gov/downloads/medicaldevices/productsandmedicalprocedures/in VitroDiagnostics/UCM584603.pdf MSK-IMPACT Decision summary: https://www.accessdata.fda.gov/cdrh_docs/reviews/den170058.pdf Oncomine Dx Target Test SSED: https://www.accessdata.fda.gov/cdrh_docs/pdf16/p160045b.pdf F1CDx SSED: https://www.accessdata.fda.gov/cdrh_docs/pdf17/p170019b.pdf 27