Enterprise Interest Thermo Fisher Scientific / Employee

Enterprise Interest Thermo Fisher Scientific / Employee

A next-generation sequencing assay to estimate tumor mutation load from FFPE research samples Fiona Hyland. Director of R&D, Bioinformatics Clinical Next-Generation Sequencing Division 2 For Research Use Only. Not for use in diagnostic procedures. The world leader in serving science

Mutation Load correlates with response to Immunotherapy High mutation load correlates with patient response to CTLA- 4 and PD-1 inhibition Highly mutated tumors are more likely to harbor neo-antigens which make them targets of activated immune cells. DCB: Durable Clinical Benefit NDB: No Durable Benefit From Rizvi et al., Science, 2015 Mutation Load : Number of somatic mutations per Megabase 3 For Research Use Only. Not for use in diagnostic procedures.

Thermo Fisher Scientific s NGS Oncology Portfolio Category 1 25 Genes 26 100 Genes > 100 Genes Solid tumor profiling Oncomine BRCA Research Assay Somatic mutations + germline Oncomine Focus Assay 50 DNA genes + 23 RNA genes; hotspots, indels, CNVs, Fusions Ion AmpliSeq Cancer Hotspot Panel v2 50 genes; hotspots, indels Oncomine Comprehensive Assay 143 genes, hotspots, indels, CNVs, Fusions Ion AmpliSeq Comprehensive Cancer Panel 400 genes Heme-Onc profiling Ion AmpliSeq AML Research Panel 19 genes Oncomine Myeloid Research Panel coming soon Oncomine Childhood Cancer Research Panel (In Development) Oncomine cfdna Lung Assay 11 genes, hotspot driver mutations Oncomine cftna PanCancer Assay (In Development) Oncomine cfdna Colon Assay 14 genes, hotspot driver mutations Liquid biopsy cfdna solutions Immuno-Oncology (IO) solutions Custom Oncology solutions Oncomine cfdna Breast Assay 10 genes, hotspot driver mutations Oncomine Lung cell free Total Nucleic Acid Assay 12 genes, hotspots, indels, CNVs, Fusions coming soon Enhanced Oncomine cfdna Breast Assay 12 genes, hotspots, indels, novel TP53, CNVs coming soon Oncomine Immune Repertoire Research Assay Ion AmpliSeq Custom Panels Oncomine Tumor Mutation Burden Research Assay (In Development) Oncomine Immune Response Research Assay 395 genes, expression assay 4 For Research Use Only. Not for use in diagnostic procedures.

In silico Correlation of Mutation Load between Exome Sequencing and a 400-gene Targeted panel using TCGA data Mutation Count with Gene Panel Ion AmpliSeq Panel: 409 Genes (1.7 MB) Mutation Count through Exome 5 For Research Use Only. Not for use in diagnostic procedures.

In silico Correlation of Gene panel with Exome, by Cancer Type For most cancer types, mutation load estimate by Gene Panel strongly correlates with exome sequencing 6 For Research Use Only. Not for use in diagnostic procedures.

Oncomine Tumor Mutation Load Research Assay 2x8hr Clinical Research Workflow Prep Sequence Analyze Library Prep Template Prep Sequencing Analysis Ampliseq Assay Ion Chef System Ion S5 and Ion S5 XL Systems Tumor Mutation Burden workflow in Ion Reporter Software FFPE or FF (fresh frozen) 10ng DNA Mutation Load per Mb Panel: Ion AmpliSeq Panel (for example, a 400-gene panel) Variant Type: SNPs at >= 5% allelic frequency Analysis: Ion Reporter Workflow; variant calling, noise filtering, germline filtering, reporting Germline filters: 1000 Genomes, 5000 Exomes, UCSC Common SNPs, ExAC 7 For Research Use Only. Not for use in diagnostic procedures.

Goals Accurate estimate of Mutation Load Workflow for Tumor Only : eliminate need for a matched normal sample (Tumor Normal) Works on FFPE samples, as well as Fresh Frozen Low input amount (10ng DNA) Reproducible Separate High mutation load from Low mutation load samples 8 For Research Use Only. Not for use in diagnostic procedures.

Somatic mutations in Tumor-only analysis echos Tumor-normal Single-sample analysis, # somatic mutations Correlation of somatic mutations r = 0.9197 Tumor-normal analysis, # somatic mutations 9 For Research Use Only. Not for use in diagnostic procedures.

Reproducible mutation load, Fresh Frozen and FFPE # Somatic Variants # Somatic Variants 30 25 CRC 40 35 SCLC 20 30 25 15 20 10 15 5 10 0 FF FFPE 5 0 FF FFPE P=0.56 P=0.58 10 For Research Use Only. Not for use in diagnostic procedures.

Reproducible mutation load (Oncomine TM Comprehensive Assay) Mutations/ Mb Bladder Brain Colon Head & Neck Lung Ovary Stomach Uterus NCI-H647 Reproducible mutation counts 11 For Research Use Only. Not for use in diagnostic procedures.

TMB can separate High and Low Mutation Load Samples Somatic mutations High Mutation Load MSI (Microsatellite instability) - Impaired MMR genes increases somatic mutations Mutation burden in MSI/MSS research samples Low Mutation Load MSS (Microsatellite stability) No impaired MMR genes, no increase in somatic mutations P-value = 1.984e-09 MSI MSS Ampliseq TMB panel and analysis solution on collaborator FFPE tumor samples with known MSI status successfully separates high and low MSI samples with statistically significant difference in means 12 For Research Use Only. Not for use in diagnostic procedures.

Mutation Load Result Report Mutation Load Analysis Workflow Information Sample Information QC Information Allele Ratio Distribution Plots and Somatic Mutation Characterization 13 For Research Use Only. Not for use in diagnostic procedures.

Mutation Load Result Report Mutation Report Bar chart representing frequency of somatic mutations in 96 mutation type classification based on 6 substitution classes, and 5 and 3 base for each variant. Left pie chart divides somatic mutations into 6 base substitution classes based on their substitution type Right pie chart divides somatic mutations in groups consistent with specific mechanisms, such as UV damage, tobacco smoke damage, and spontaneous de-amination of 5- methylcytosine 14 For Research Use Only. Not for use in diagnostic procedures.

Measuring Mutation load with next-generation sequencing In development - Accurate, reproducible quantification of somatic mutations for tumor mutation burden in research samples Single sample workflow (tumor only, no need for matched normal) FFPE, low input DNA requirement Stratify High from Low Targeted Ion Ampliseq NGS panel with high multiplexing ability Simple, optimized end-to-end workflow 15 For Research Use Only. Not for use in diagnostic procedures.

Thermo Fisher Ruchi Chaudhury Warren Tom Iris Casuga Janice Au-Young Asha Kamat 2017 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. 16 For Research Use Only. Not for use in diagnostic procedures.