1. Ensuring the Quality of Genetic Testing ICORD Meeting September 14, 2007 Lisa Kalman, PhD Coordinator, GeT-RM CDC LKalman@cdc.gov

2. How does the genetic testing laboratory know that a test is working properly and will give accurate results?

3. Reference or Quality Control (QC) materials are used to: Assess whether the genetic test is working Assess whether the genetic test is working properly and can detect genetic alterations (mutations) Quality Control

4. What is the Ideal Reference Material for Genetic Testing? (Ideally) Blood from patients with characterized mutations or alleles known to cause the disorder (Practically) Material that closely resembles a patient sample so it can be used to monitor and evaluate all steps of the testing process (Practically) Material that closely resembles a patient sample so it can be used to monitor and evaluate all steps of the testing process  Could be a cell line or purified DNA  Studied extensively and proven to contain particular mutations(s) (alleles)

5. Reference materials are also important for: Comparison of results between laboratories Comparison of results between laboratories Proficiency testing samples Proficiency testing samples Test calibration Test calibration Development of new genetic tests Development of new genetic tests Validation of new genetic tests Validation of new genetic tests

6. Reference Materials for Genetic Testing Genetic testing volume is increasing Genetic testing volume is increasing Many new tests are being introduced Many new tests are being introducedHowever….. Positive controls samples are NOT publicly available for most genetic tests! (and even fewer have been verified) verified)

7. Collected information about 35 US testing labs All clinical labs tested for at least the ACMG All clinical labs tested for at least the ACMG recommended 23 CF alleles recommended 23 CF alleles Identified 102 different CF alleles tested in US Identified 102 different CF alleles tested in US clinical labs  There are cell lines for only 42 alleles  60 alleles not available as cell lines ! Example - Cystic Fibrosis (CF) Genetic Testing

8. Other Examples Fragile X and Huntington Disease Genetic tests where the size of the gene is measured Genetic tests where the size of the gene is measured VERY technically difficult tests VERY technically difficult tests Precise size measurement is needed for proper diagnosis Precise size measurement is needed for proper diagnosis Few characterized reference materials available!

9. When No Reference Materials are Available….. Labs use previously assayed patient samples Labs use previously assayed patient samples  Problem-how do you know that they were assayed correctly if the lab lacks controls? Synthetic controls are available for a few tests Synthetic controls are available for a few tests  Problem- synthetic DNA may not perform the same as human DNA in the assay Sometimes labs run assays without adequate controls Sometimes labs run assays without adequate controls  Problem- not ideal, may increase chance of errors!

10. Genetic Testing Reference Material Program (GeT-RM) A CDC-based program to improve the availability of reference materials for genetic testing Collaboration with genetic testing community Academic and clinical genetic testing labs Academic and clinical genetic testing labs Government agencies Government agencies Cell repositories Cell repositories Industry Industry Professional organizations Professional organizations

11. Roles of GeT-RM Improve and coordinate information exchange about reference materials Improve and coordinate information exchange about reference materials Monitor reference material needs of genetic testing community Monitor reference material needs of genetic testing community Facilitate submission, development and characterization of reference materials Facilitate submission, development and characterization of reference materials Develop a sustainable community process for continued reference material development Develop a sustainable community process for continued reference material development

13. GeT-RM Website http://wwwn.cdc.gov/dls/genetics/qcmaterials/default.aspx Provides information about: Provides information about: Availability and validation status of a variety of reference materials Availability and validation status of a variety of reference materials Reference material needs Reference material needs How to contribute potential reference materials How to contribute potential reference materials Professional and regulatory guidance Professional and regulatory guidance References References CDC’s efforts to improve the quality of genetic testing CDC’s efforts to improve the quality of genetic testing Solicits input from the genetic testing community Solicits input from the genetic testing community

14. Coriell Institute for Medical Research http://ccr.coriell.org/Default.aspx http://ccr.coriell.org/Default.aspx National Institute of General Medical Sciences (NIGMS) Human Genetic Cell Repository http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8 Non Profit -Supported by NIH Non Profit -Supported by NIH Coriell distributes DNA and cell line samples to facilitate genetic research and improve laboratory quality since 1972 Coriell distributes DNA and cell line samples to facilitate genetic research and improve laboratory quality since 1972

15. GeT-RM Reference Material Development Projects

16. Ashkenazi Jewish Panel Recently completed characterization of 27 cell lines from Coriell as reference materials for genetic testing of 9 disorders common in the Ashkenazi Jewish population Tay-sachs disease Tay-sachs disease Canavan disease Canavan disease Glycogen storage disease type 1a Glycogen storage disease type 1a Familial dysautonomia Familial dysautonomia Mucolipidosis type IV Mucolipidosis type IV Niemann-Pick disease type A Niemann-Pick disease type A Fanconi anemia group C Fanconi anemia group C Bloom syndrome Bloom syndrome Gaucher disease Gaucher disease

17. Huntington disease and Fragile X The GeT-RM has completed characterization of: 14 Huntington cell lines from Coriell 14 Huntington cell lines from Coriell 21 fragile X cell lines from Coriell 21 fragile X cell lines from Coriell For use as reference materials!

18. GeT-RM Current and Future Reference Material Development Projects Cystic fibrosis Cystic fibrosis Breast Cancer Breast Cancer Newborn Screening disorders Newborn Screening disorders Others??? Others???

19. Continued Reference Material Development… Material Development… Big Problem… Lack of available cell lines!!!!!

20. Development of New Reference Materials 2 Methods 2 Methods 1. Establish new cell lines 2. Identify mutations in existing cell lines Problem- Limited access to patient blood samples!

21. GeT-RM is expanding into other areas of molecular testing - Molecular Oncology Molecular Oncology Infectious Disease Infectious Disease Biochemical Genetic Tests Biochemical Genetic Tests

22. ! GeT-RM : http://wwwn.cdc.gov/dls/genetics/qcmaterials/default.aspx http://wwwn.cdc.gov/dls/genetics/qcmaterials/default.aspx