Defining Actionable Novel Discoveries, Annotating Genomes, and Reanalysis in Cancer A Laboratory Perspective

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1 Integrating Large-Scale Genomic Information into Clinical Practice: A Workshop Defining Actionable Novel Discoveries, Annotating Genomes, and Reanalysis in Cancer A Laboratory Perspective Federico A. Monzon M.D. Associate Professor of Pathology, Weill-Cornell Medical College, New York NY Genomic Pathologist, Molecular Diagnostics Director, Molecular Genetic Pathology Fellowship The Methodist Hospital, Houston TX Director, Research Pathology and Molecular Diagnostics Cores The Methodist Hospital Research Institute, Houston TX

2 Outline Genomic Testing in Cancer Background Issues created by the genomics approach Analysis of Cancer Genomic Data Novel Discoveries Updating previously analyzed data Coping with the issues 2

3 Breast Cancer Testing Evolution Morphology Single biomarkers ER in Breast Cancer Biomarker Panels ER/PR/ERBB2(Her2) Expression Profiles Oncotype DX, Mammaprint, Intrinsic subtypes Targeted sequencing BRCA1/2, PIK3CA, TP53, MAP3K1, ATR, MYST3. Exome sequencing Whole genome sequencing 3

4 Laboratory Perspective Analysis issues created by genomic testing Clinical Validation (i.e. does my test identify the right patient?) Current standards for validation do not apply to multianalyte tests, much less whole exome/genome Responsibility of laboratory director How many patients/tumor types per variant detected? Regulatory environment is not well defined yet We need a balance between: Standards and regulations that ensure quality of genomic testing Standards and regulations that stifle innovation 4

5 Laboratory Perspective Analysis issues created by genomic testing Analytical Validation (i.e. do I detect what I m supposed to?) Can I detect all described variant transcripts/mutations/sequences? Do I need to represent all possible variants in my validation studies? Do I need to validate all genomic regions interrogated? There are cost and sample access issues that limit what is feasible What is the gold standard? Sanger sequencing Most genetic variants detected with NGS have not been reported before 5

6 Laboratory Perspective Analysis issues created by genomic testing What do I report? What is the standard for clinical significance in cancer? Tiered reporting: Actionable, Potentially significant, Risk variants, Unknown significance Shifting knowledge When does a finding changes categories (potentially>actionable)? Who is going to be responsible for curating databases for actionable data? Who s responsibility is to ensure that all labs use the latest data? Is our guideline process through national groups (CAP/ASCO/NCCN) capable of coping with the anticipated growth in data? See Blanke et al. Oncologist

7 Current Example 7

8 Chronic Lymphocytic Leukemia Five main genetic aberrations are recognized in CLL with major impact on disease behavior. From Gerson and Keagle, The Principles of Clinical Cytogenetics, 2 nd Ed, Humana Press, p473 Several clinical validation studies have shown SNP arrays have >95% concordance with the standard CLL FISH panel. In addition, many studies using array-based karyotyping have identified 'atypical deletions' missed by the standard FISH probes and acquired uniparental disomy at key loci for prognostic risk in CLL. Hagenkord JM, et al. Array-based Karyotyping for Risk Assessment in Chronic Lymphocytic Leukemia: Performance Comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 Arrays.J Molec Diagn (2010) 8

9 CLL with Genomic Complexity Is this an actionable result? Genomic Complexity has been recently linked to poor outcomes Described in 112 of 625 patients (by cytogenetics) and in 50 of 178 (by cytogenomic arrays) What level of evidence is required to direct medical decisions? What intervention will be performed? Whole exome/genome will further complicate these issues 9

10 How do we tackle the issues? Validation Guidelines, regulations and standards Sequencing application/instrument approvals vs. individual tests Reporting Defining what is clinically relevant (actionable results) might depend on available interventions (therapies) Databases on clinical utility of cancer variants linked to therapeutic agents (with oucome data) One step at a time in the clinical environment Accumulate information from targeted assays to increase knowledge understanding (driver vs. passenger variants) Move to whole genome 10

11 Shifting Knowledge Physician s responsibility to deliver standard of care = updating reports with latest discoveries? Laboratory directors are not adequately resourced for Genomic Medicine Access to curated information Reimbursement for updating report activity (professional component is non-existent in many clinical tests, much less updating activities) Define algorithms for report updating and to judge impact/significance for the patient Smart laboratory information systems 11

12 Questions? 12 TMHRI by Aker/Zvonkovic Photography

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