1. Another Look at Free Markets – Regulating and Evaluating Genetic Tests Lawrence Silverman May 30, 2009 Oversight of Genetic tests – Roles of FDA, CDC, and CMS and their relationship with CLIA? How Are Genetic Tests Assessed? - What is Analytical Validity, Clinical Validity, Clinical Utility, and Quality Assurance What is Evidence-based Medicine and EGAPP

2. Oversight of Genetic tests – Roles of FDA, CDC, and CMS and their relationship with CLIA? Or, “It’s Just as Good as a Sony” How Are Genetic Tests Assessed? - What is Analytical Validity, Clinical Validity, Clinical Utility, and Quality Assurance Or, Just Because We Can Perform a Genetic Test, Should We? What is Evidence-based Medicine and EGAPP Or, Bian Hua (Things Change) Another Look at Free Markets – Regulating and Evaluating Genetic Tests

3. Clinical Laboratory Improvement Amendment Passed in 1988 (enacted in 1992) and regulates all clinical laboratory testing aspects. Center for Medicare and Medicaid Services (CMS) - responsible for CLIA oversight, including financial management of CLIA operations FDA has oversight for laboratory tests under CLIA CDC serves an advisory role on CLIA, primarily through CLIAC (Clinical Laboratory Improvement Advisory Committee)

5. PCR described Molecular Diagnosis of Sickle Cell Anemia using PCR 1985 1986 Linkage analysis for CF, DMD, Hemophilia A&B Dystrophin gene cloned 1987 1988 Direct testing for DMD CFTR gene cloned 1989 Direct testing for CF Human Genome Project starts 1990

6. Regulation of Genetics Tests Hot button item IOM – 1994 Task Force on Genetics Tests – 1997 Secretary’s Advisory Committee on Genetic Tests – 2001 – analytical validity, clinical validity, and clinical utility. Regulatory gaps

7. What are Key Issues in Assessing Genetic Tests Analytical Validity – does the test measure the analyte in question i.e., can the test detect both the presence and absence of mutations. Clinical Validity – does the test result predict the presence or absence of disease Clinical Utility – how does the test result affect morbidity, mortality, or disability, specifically through treatments based on the test result.

8. What is a genetic test and how are they used? Genetic tests refer to the measurement of DNA, RNA, chromosomes or proteins that reflect changes in genes or gene products that are associated with specific disorders or phenotypes. These disorders may be heritable or acquired. How genetic tests are commonly used: Newborn screening, diagnostic testing, carrier testing, prenatal testing, preimplantation testing, predictive and presymptomatic testing, identity and forensic testing. Predictive testing includes pharmacogenomics.

9. Developing Regulatory Requirements for Genetic Testing Under CLIA Recommendations were made to CLIAC on modifying CLIA to include a genetic testing specialty. Scope included definitions and requirements for pre-analytic, analytic and post-analytic phases of testing – 1997-1999 Notice of Intent (NOI) – Published in Federal Register 5/2000 notifying that a Notice of Proposed Rule Making was being prepared to revise CLIA in order to make a human genetics testing specialty. 57 responses comments were received in response to NOI CLIAC Workgroup on Genetic Testing makes recommendations to public response - 2/2001. CMS puts issuance of specialty area on regulatory agenda with release date of November – 4/2006 CMS decides a genetic testing specialty is unnecessary since existing CLIA regulations are sufficient (“It’s just as good as a Sony”) – 9/2006

10. How Are Genetic Tests Different – Let Me Count the Ways Penetrance Expressivity Modifiers Epigenetics De Novo versus inherted Impriniting Discrimination (perceived) Association v causality Privacy v right to know Presymptomatic Predictive Lack of PT Surveys

11. Hudson K., J. Murphy, D. Kaufman, G. Javitt, S. Katsanis, and J. Scott. 2006. Oversight of US Genetic Testing Laboratories. Nature Biotechnology 24 (9): 1083-1090. 2006 Survey of Genetic Testing Laboratory Directors Collect data on genetic testing laboratory PT practices Evaluate participation in PT and laboratory quality Assess views of genetic testing laboratory directors

12. Survey Results 95% of molecular and biochemical testing labs reporting results to patients are CLIA certified 35% of laboratories do not do PT for all of the tests they perform 73% of genetic testing laboratory directors in this survey support CLIA specialty

13. FDA and the ASR Rule However, FDA has chosen only to regulate the ingredients of LDTs (ASRs) since “CLIA regulated labs qualified to perform high complexity testing have demonstrated expertise and ability to use ASRs in test procedures and analyses.” “It’s Just as Good as a Sony” “Clinical laboratories that develop tests are acting as manufacturers of medical devices and are subject to FDA jurisdiction”. ASR – Analyte Specific Reagent used in laboratory developed tests (LDT)

14. EGAPP Evaluation of Genomic Applications in Practice and Prevention In 2004 CDC established EGAPP to evaluate a systematic, evidence-based process for assessing genetic tests and other applications of genomic technology in transition from research to clinical and public health practice. EGAPP utilizes ACCE criteria (Analytic and Clinical validity, Clinical utility and associated Ethical, legal, and social implications) developed by Foundation for Blood Research in 2004. Published Recommendations: Can Tumor Gene Profiling Improve Outcomes in Patients with Breast Cancer Can UGT1A1 Genotyping Reduce Morbidity and Mortality in Patients with Metastatic Colorectal Cancer Treated with Irinotecan Genetic Testing Strategies in Newly Diagnosed Individuals with Colorectal Cancer Aimed at Reducing Morbidity and Mortality from Lynch Syndrome in Relatives

15. What are Limitations of EGAPP (and ACCE) Clinical Validity is not regulated under CLIA, which only regulates performance specifications, such as accuracy, precision, reportable ranges and reference ranges. Professional organizations or state agencies that have clearance to inspect and accredit laboratories can exceed CLIA specifications, thus, make requirements regarding establishment of clinical validity. However, this is not universal. Clinical Utility is both nebulous in definition and dependent on changing technology, clinical knowledge, and therapy. Thus, Bian Hua, things change.

16. Fragile X Premutation and Ovarian Dysfunction Fragile X Syndrome - Most common cause of inherited mental retardation Affects 1:2500-1:4000 males Affects 1:5000-1:10000 females X-linked mental retardation

17. 1) Mental Retardation-IQ<50 in affected males, IQ 70-90 in affected females 2) Characteristic Facies -low set ears, prominent jaw 3) Behavioural abnormalities -hyperkinetic -autistic like behaviour -learning disabilities 4) Macroorchidism

18. -Fragile Site induced by culturing in folate depleted media -Cytogenetic analysis positive in about 60% cases only -High degree of variability between labs and individuals -False positives due to other fragile sites in the vicinity

19. FMR-1 (CGG)n >200 55–200 45-54 5–44 Normal Premutation (not hypermethylated) Full mutation (inactive, hypermethylated) CpG EcoRI NruI Active Inactive 2.8 kb 5.2 kb Fragile X Syndrome Molecular Diagnostics “Grey Zone”

21. Fragile X Sizing in Males Normal Male 12 CGGs Premutation Male 89 CGGs

22. Fragile X Sizing in Females Normal Females 28/37 CGGs Premutation Female 28/78 CGGs

23. Fragile X Premutation Defined as CGG between 55-200 Not hypermethylated; gene not shut down Individuals do not have fragile X syndrome Males with premutations pass on only premutations to their daughters Likelihood of passing full mutation from mother to offspring increases with size of premutation; 100% likelihood by 90 CGGs

24. Frequency of Fragile X Premutation Differs from study to study In women-1:100 to 1:250 In men-1:250 to 1:750

25. Premature Ovarian Failure (POF) Mean age of menopause is about 51 POF defined as menopause before age 40 About 1% of females have POF Elevated FSH/LH ratios Both genetic and environmental causes known However, 60% of cases have no obvious cause

26. POF in Fragile X Carriers Increased rates of POF found only in premutation carriers About 16-20% of premutation carriers have POF Full mutation carriers have no higher incidence of POF High FSH levels (> 15 IU/L) often found in menstruating women prior to POF No changes in inhibin B or 17β estradiol levels

27. POF in Fragile X Carriers Screening of all POF patients led to a pick up rate of about 1.6-8% for FRA-X premutations Repeat number ranged from 80-175. No full mutations were identified

28. POF and Fragile X Premutation Pick up rate for premutation in familial POF is much higher; about 14-18% In sporadic POF 2-4%

29. What About Premutation Male Carriers? FXTAS- a new neurologic phenotype Several studies have now described the presence of a late-onset neurological problem in males carriers of the premutation (now termed FXTAS) Cerebellar ataxia and intention tremor Other features: short term memory loss, cognitive decline, parkinsonism, autonomous dysfunction, executive functional defects MRI shows approx. symmetric increases in T2 weighted signal intensity in middle cerebellar peduncle Eosinophilic intranuclear inclusions found in neurons and astrocytes Increasing penetrance of the phenotype with age; >80% by age 80 Females also affected but severity and penetrance are less

30. Jacquemont, S. et. al., JAMA-Jan. 2004

31. Summary of Regulatory Gaps Lack of Genetics Specialty under CLIA Lack of FDA oversight for LDT (except ASR) Uncertainty regarding clinical validity and clinical utility Inadequacy of PT Surveys for most genetic tests Insufficient transparency regarding laboratory performance