Adding Clinical Services to a Research Core Lab at the UW-Madison. Josh Hyman, Director UWBC DNA Sequencing Facility

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1 Adding Clinical Services to a Research Core Lab at the UW-Madison Josh Hyman, Director UWBC DNA Sequencing Facility

2 Impetus UW researchers/clinicians becoming interested in moving more discoveries from research studies to the clinic. UW Hospital and Clinic outsourcing many tests. Outside entities, both public and private, inquiring about accreditation.

3 The Long Road to CLIA Registration Staffing (qualifications, training, competency) Protocol versioning (modular) Reagent validation and tracking Detailed electronic record keeping (staff skills, instruments, reagents, workflows, samples) Service validation (analytical) and proficiency testing Clinical validation Reporting

4 Staffing Clinical Laboratory Technician Laboratory Supervisor Clinical Laboratory Director

5 Staffing Clinical Laboratory Technologist/Technician: A clinical laboratory technologist/technician must hold an undergraduate degree in a relevant scientific field or have at least 5 years of relevant laboratory experience. > No undergraduates can handle samples. > No one with an associates degree can handle samples unless they have relevant laboratory experience. Seems to some discrepancy regarding the above.

6 Staffing Clinical Laboratory Supervisor: A laboratory or general supervisor must hold a Bachelors degree and have had at least 3 years of experience in medical/genetics laboratory under the supervision of a qualified laboratory director or technical supervisor.

7 Staffing Clinical Director: A laboratory director and/or technical supervisor must have an appropriate doctoral degree and at least 2 years of postdoctoral training and/or experience in his/her clinical laboratory subspecialty, and either American Board of Medical Genetics (ABMG) certification or eligibility in the specific specialty, or for molecular genetic testing only, the conjoint American Board of Medical Genetics and American Board of Pathology subspecialty certification in molecular genetic pathology

8 Differing Levels of Authority The Lab Director may be different than the Clinical Lab Director. The Lab Director defers to the authority of the Clinical Lab Supervisor or the Clinical Lab Director in matters pertaining to clinical sample processing. All parties need to understand their boundaries and that may need to be spelled out (federal research versus clinical).

9 Protocol and Workflow SOPs Get rid of lab notes. No Sticky notes. Use only the official copy of the SOP. Modularize. Smaller protocols within workflows. Perform each discrete process, recording all pertinent details Have someone read the detailed description while observing, asking questions, and adding more detail Have other technicians perform the protocol while observer watches for alternate interpretations

10 Reagents Reagent expiration dates must be followed. All reagents MUST have expiration dates unless RUO. Bench reagents generally have one week. Reagent lot number used for processing a sample must be recorded. Reagent lot integrity must be maintained, no mixing. New reagent lots must be validated to have same performance as previous lots. (cost)

11 Instrument Maintenance by Facility or Vendors Semiannual testing/certification Thermocyclers, calibration eqpt certified annually Pipettes Fluorometers Annual testing/certification Sequencers Centrifuges Any changes/upgrades require testing/validation

12 Staff Training Protocols are detailed on SOPs Individual responsible for the initial protocol trains other technicians (SLH?) Student observes the protocol being performed Performs three times under observation and guidance of responsible individual Perform three times unsupervised without errors Competency testing semi-annually for first year and then annually

13 Everything has an SOP Training Maintenance QA/QM Every clinical assay

14 Record Everything Electronically ipassport Training Maintenance SOPs LIMS Every sample Every workflow Windopath Case processing and tracking

15 Validating Services No service can be on the menu that is not validated Established CLIA services have standards for testing Next generation sequencing has no standards that can cover every mutation Smaller panels may be more manageable when it comes to acquiring standards (synthetic?)

16 Validating Services Sensitivity True positive / (True positive + False negative) Specificity True negative / (True negative + False positive) Some mutations are extremely rare. Given the number of loci we are testing, how many samples will we realistically need to test?

17 Proficiency Testing CAP has Proficiency Testing programs, but not for NGS. Alternative Performance Assessment may include split sample testing with another lab. Who performs the same test across the same loci? Identify labs with equivalent service Negotiate PT arrangement (cost, reporting, timing)

18 Clinical Validation ClinVar, Research networks (PGRN), annotated databases, FDA imposed framework Our collaborators are responsible for this. We do not have the expertise.

19 Reporting Clinical Lab Director reviews and signs off Bioinformaticians process the data Results are compared against annotated databases, current and accepted research Reporting tools can be used for more intensive comparisons (Cartagenia) Our collaborators are responsible for this. We do not have the expertise.

20 Integrating Clinical Services in a Research Core Lab Collaborate, you will need the experience and resources from multiple departments. Evaluate both your staffing and your record keeping resources to identify weak points. Take your time, this is a system with many moving parts. Learn to enjoy endless hours of reading and interpreting regulations.

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