MOLECULAR TESTING: VERIFYING/VALIDATING INSTRUMENTS, REAGENTS AND ASSAYS. Richard L. Hodinka, Ph.D.

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1 MOLECULAR TESTING: VERIFYING/VALIDATING INSTRUMENTS, REAGENTS AND ASSAYS Richard L. Hodinka, Ph.D. University of South Carolina School of Medicine Greenville Greenville Health System, Greenville, SC WS2-3

2 Objectives List components of the verification and validation processes Describe the process of verifying an FDAcleared or approved molecular assay Describe the process of validating a modified or laboratory-developed molecular assay

3 Clinical Test Formats Two major formats used in laboratories that perform molecular diagnostics: Assays developed by the manufacturer IVD products Laboratory developed tests (LDTs)

4 Manufacturer-Developed Assays Unmodified FDA-cleared Composed of kits and instrumentation for the performance of the entire molecular test for a given clinical condition Includes quality-controlled reagents needed for nucleic acid isolation, amplification, and detection/quantification and automation to complete the steps of the procedure Modified FDA cleared Modified by laboratory Performed outside scope of package insert instructions

5 Laboratory Developed Assays Synonymous with in-house or home-brew tests; developed by the end user Has not been cleared by FDA Use a combination of reagents that are either purchased commercially from various vendors or produced in-house General purpose reagents Analyte-specific reagents (ASRs) RUO reagents Any procedure that incorporates changes of a manufacturer s package insert Any method in which performance specifications are not provided by the manufacturer

6 Molecular-Based Technology for ID Testing Laboratory-Developed Assays: Clinical Specimens Extraction Amplification Detection Amplification & Detection Results FDA-Cleared: Drive Towards Fully Integrated and Automated Systems: Molecular Diagnostic Device Clinical Specimens Pandora s box.. Results

7 Processes of Verification/Validation Verification A one time process completed during assay development to determine or confirm test performance characteristics before test system is used for patient testing Validation Ongoing process; action of proving that a procedure, process, system, equipment, or method used continues to work as expected and achieves intended result; Components of validation are QC/QA, PT, competency, instrument calibration, and correlation with clinical findings Much debate about what is acceptable

8 Purpose of Verification/Validation Satisfy regulatory requirements CLIA sets minimum standards that must be met in verifying/validating performance of clinical tests Each laboratory must demonstrate reproducible performance characteristics in their own laboratory Objective is to ensure accuracy, reliability, and appropriateness of clinical test results, regardless of where testing is performed

9 When Do You Verify? Detect or identify a totally new analyte A new approach to detecting an analyte Change from manual method to automated one A new application of existing technology A new matrix (old analyte in different specimen) New or improved reagents or instruments Using an IVD test off-label May be necessary even for minor changes

10 Performance Characteristics As applicable, must include the following: Accuracy Precision Analytical Sensitivity Analytical Specificity (including interfering substances) Reportable Range Reference Range (normal values) Linearity (for quantitative assays) Any other performance characteristic needed

11 FDA-Approved Tests Method verification - Prove that performance specifications established by manufacturer can be reproduced in laboratory for population of patients served Performance characteristics that must be verified: Accuracy (clinical sensitivity and specificity) Precision Reportable Range Reference (Normal) Range Not required to verify analytical sensitivity or analytical specificity Should verify limit of detection (LOD) for quantitative assays

12 Laboratory-Developed Tests More extensive studies required Must establish performance specifications of test at time of test development Performance characteristics to be established: Accuracy Precision Analytic Sensitivity Analytic Specificity Reportable Range Reference Interval

13 Desirable Attributes: LDTs What do we want? Consistently produces accurate results Reproducible over extended periods of time Rapid turnaround time for maximum impact Provide a less expensive or more effective diagnosis for appropriate patient care and management

14 The Fun of LDTs What are the issues? LDTs are not reviewed by regulatory agencies Laboratory is fully responsible for defining the performance characteristics of each developed assay Implementation of an LDT is an involved process with extensive experimentation and documentation End user is essentially acting as a manufacturer of medical device and is responsible for both the suitability and correct performance of test Considerable verification and validation needed

15 Accuracy Technical Accuracy - nearness of an individual measurement to the true value Clinical Accuracy - overall ability of a test to both rule in and rule out an analyte or specific disease Synonymous with test efficiency Do Comparison of Methods Study Analyze samples with known target value or test samples in parallel with valid alternative method; 90% agreement Agreement with reference method

16 Typical Study Design Directly compare new test to gold standard Use patient samples Test prospectively Challenge panels and proficiency samples also may be used Testing by both methods should be done at nearly the same time

17 Specimens for Evaluation Should be typical of those that will be routinely tested Volume should be enough to complete testing with test method and comparative method and to store for discrepant analysis Only use specimens that have been properly collected, transported, processed, and stored

18 Specimens for Evaluation Own patient specimens Current test serves as reference method Split and send to outside lab for ref method Patient specimens from another lab (or vendor) Old proficiency samples, QC or calibrators Should be in appropriate matrix, and have analyte in clinically relevant concentrations Spiked samples (own lab, or provided by vendor) Appropriate matrix, and analyte in clinically relevant concentrations

19 Number of Specimens Testing should continue until at least 50 positive specimens are obtained At least 100 negative specimens should be tested Depending on disease prevalence, evaluation can be more or less difficult More samples and more measurements provide better estimates Minimum of 20 specimens (mix of positive and negative)

20 Duration of Evaluation Comparison of methods with clinical specimens should be conducted daily for at least 10 to 20 days Allows user to test method under typical laboratory operations and to obtain representative number of specimens

21 Control of Inhibition (LDTs) Need to control for inhibition Decide during test evaluation Monitor combined effect of extraction and amplification Use exogenous controls or house-keeping genes (e.g., albumin, -actin, GAPDH) Can multiplex in same tube or run separate reactions

22 Discrepant Results Due to errors in test method or reference method that is not 100% Retest samples in duplicate using both methods (discouraged) If reference method is not 100%, use accepted third method to resolve discrepancy Sequencing Review clinical information, if needed

23 Data Analysis Sensitivity (TP/TP+FN x 100) Specificity (TN/TN+FP x 100) PVP (TP/TP+FP) PVN (TN/TN+FN) Efficiency (TP+TN/TP+FP+TN+FN) Prevalence (TP/TP+FP+TN+FN)

24 Reproducibility Studies Within run Between run Day-to-day Lot-to-lot Tech-to-tech Samples Controls Calibrators Standards National and International Reference Materials Extract and test high, moderate, and low level materials Measure precision in terms of standard deviation (SD) and relative standard variation (coefficient of variation, CV)

25 Precision Measure of the extent to which an assay produces the same result when an analyte is tested in replicate within a single run (intraassay precision) and from one run to another (inter-assay precision) using identical procedures Implies freedom from inconsistency and random error; does not guarantee accuracy Synonymous with reproducibility

26 Accuracy versus Precision High Accuracy, Low Precision High Precision, Low Accuracy

27 Analytical Sensitivity Lowest amount of analyte that is reproducibly distinguishable from background (a negative control) with a stated level of confidence Level of confidence is usually set at 95%; the amount of target that can be detected 95% of the time ( 2 SD) Referred to as Limit of Detection (LOD) Perform dilution series using known amounts of analyte

28 Limit of Detection (LOD) Applied to both quantitative and qualitative tests Indicates that at least 95% of the time the given concentration of analyte can be distinguished from a negative sample LOD is expressed usually in copies/ml, copies/ug, IU/ml; lower the detectable concentration of analyte, the greater the analytical sensitivity of the assay Verify using 20 data points collected over 5 days

29 Limit of Detection Calculations Linnet & Kondratovich formula power curves PROBIT Analysis Reed and Meunsch Method CLSI EP17-A Protocols for Determination for Limits of Detection and Limits of Quantitation; Approved Guideline 2004

30 Probit Analysis Limit of Detection c/ml 95% Confidence Interval 6.65 Probit Value Log10 copy no. No. of replicates Number positive Percent positive Probit value N/A N/A N/A N/A Log 10 of the concentration detectable 95% of the time 1.90 Reed and Muensch Limit of Detection c/ml Log10 copy no. No. of replicates Concentration detectable 95% of the time Number positive Number negative Cum positive Cum negative Percent positive Log 10 of the concentration detectable 95% of the time 2.01 Concentration detectable 95% of the time

31 Limits of Quantification (LOQ) Lowest (LLOQ) and highest (ULOQ) concentrations of analyte that can be quantitatively determined with acceptable accuracy (total error) The LLOQ may be equivalent to the LOD or it can be at a much higher concentration The LOD cannot be higher than the LLOQ.

32 Analytical Specificity Ability of a test to detect only the analyte that assay is designed to measure In other words, the ability of the assay to produce a negative result when target nucleic acid is absent

33 Analytical Specificity Test a panel of representative (or related) organisms to determine if you get false positives Analysis of primers/probe using sequence databases (e.g., GenBank)

34 Reference (Normal) Range Background signal when testing a panel of specimens from persons believed to be free of the condition (Negative Reference Range) Range of values found in healthy persons who do not have the condition detected by the assay Specimens from uninfected patients should be NEGATIVE

35 Reportable Range Range of values that can be reported as patient results Defined by the highest and lowest calibrators used in the assay May not include the entire dynamic range of the assay

36 Linearity Determination of the linear range of quantification Define lower and upper limits of linearity Data for linearity studies should undergo linear regression analysis with ideal regression coefficient of 1

37 Handling Evaluation Data EP Evaluator Software: Accuracy, analytical sensitivity, linearity, reportable range, reference interval, precision, interference, calibration verification Qualitative method comparison Quantitative method comparison Two instrument comparison Multiple instrument comparison Cost per test

38 Multiplexed Molecular Tests May be difficult to find comparator method May be difficult to find specimen material for all analytes How many specimens to test? Single specimen platforms Commercially available nucleic acid controls Can be used to create strong and weak positives to verify reportable range; most are titered Create (spike) mixed positives to reduce the number of specimens to test Use negative patient specimens as matrix Specimen spiked with agents A, B and C serves as negative for agents D, E, F, etc.

39 Multiplex PCR Verification Example Assay detects organisms A-L (12 pathogens); NOT QUANTITATIVE Using commercially available titered controls, prepare panels, each containing 3 viruses; testing should be blinded Spike spec # Positive Neg spec for 1 A, B, C weak D-L 2 A, B, C strong e.g. Agent A has two positive specimens (1 and 2) and six negative specimens (3-8) 3 D, E, F weak A-C, G-L 4 D, E, F strong 5 G, H, I weak A-F, J-L 6 G, H, I strong 7 J, K, L weak A-I 8 J, K, L strong

40 Multiplex PCR Verification Example Supplement the spiked samples with actual patient specimens, including positives for routine agents 9 (or more) positive specimens 3 (or more) negative specimens (truly negative?) Total (patient specimens plus spiked specimens): 20 Reproducibility/Precision Select several (2-3) mixed spiked specimens to test in duplicate, and on different days with different operators Reportable/Reference Ranges Verified by obtaining expected results from spiked panels, including weak and strong positives

41 Calibration Verification Used primarily for quantitative assays; also for qualitatitve assays with declared cutoff values Calibration process of testing and adjusting an instrument, kit, or test system readout to establish a correlation between the instruments measurement of analyte being tested and the actual concentration Calibration verification assaying of calibration materials in same manner as patient specimens to confirm that calibration has remained stable over time Known quantities of a material are measured in assay and results are compared to known true value of the material

42 Calibration Verification Include two different processes Verification of previously established calibration status (setpoint) Verification of analytical measurement range (AMR) CAP requires that both be performed Calibration and AMR must be verified: every 6 months or when change of reagent lot, major instrument maintenance or replacement of critical parts, change in major assay components, control values are outside acceptable limits or show shift or drift, or laboratory establishes more frequent checks

43 Analytical Measurement Range Refers to range of values that a quantitative method can measure for a specimen without dilution, concentration, or other pretreatment of specimen prior to testing AMR is same as reportable range (CLIA) Established by linearity studies for LDTs AMR verification ensures that test system is providing accurate results throughout measurement range

44 Materials Suitable for Calibration/AMR Must have assigned concentration values Proficiency testing samples or patient specimens Commercially-available standards, calibrators, or reference materials Must have matrix characteristics appropriate for method AMR verification must done on three different concentrations (low, mid, and high values) of appropriate material Run as patient specimens

45 Other Considerations Speak with physicians and other healthcare providers Determine medical usefulness of test Will test improve patient care and/or shorten hospital stay? Is test suitable for all patient populations? Be prepared to provide physicians with specifications of test for individual populations with different diseases and prevalence

46 Other Considerations Comparative cost of method; extent of reimbursement Practicality in the laboratory setting Specimen requirements Reagents, controls, standards needed; storage requirements and shelf-life Availability of supplies, service, and/or technical support Possible safety hazards to performing test

47 Practicality in Laboratory Does test require special equipment? Can test be performed on all needed shifts? What is the turnaround time? What are the personnel requirements? Are quality control and proficiency test material available? To what extent will quality control be done? Is there adequate space? Can test be automated to reduce labor? Does system have indication for all uses of interest?

48 Validation of Tests For LDTs, conduct on final version of test protocol A continuous process Documents that a test which has already been verified is repeatedly giving the expected results as test is performed over time Confirms that test continues to perform according to laboratory s requirements and its intended use

49 Validation Process Personnel competency assessment Quality control monitoring Quality improvement Internal and external proficiency testing Correlation with clinical findings Trend analysis Integral part of a laboratory s quality assurance program

50 Price of Performing Molecular LDAs New Method Establish Performance Assay Verification Assay Validation Verify Method Method Equivalence Characterized Quality Reagents Certification Accreditation Validate Performance Quality Improvements Quality Management System Assay Implementation Implement Method Method Maintenance PT Perform Clinical Tests Internal QC Report Results Internal QA

51 Conclusions It s a challenge to ensure good laboratory practice for inhouse tests Requires substantial commitments of expertise, resources and time No stringent regulatory standards for verifying and validating; more and more guidance documents Varied approaches utilized in individual laboratories Process can be time-consuming and expensive Often complicated by paucity of specimens containing or lacking the desired analyte In some cases, laboratories make difficult choices about the extent of verification/validation Rule of Thumb studies for unmodified FDA-cleared tests can be less involved; for modified FDA-cleared tests and LDTs, must be more vigorous and extensive

52 CLSI Reference Documents MM03-A2: Molecular Diagnostic Methods for Infectious Diseases, 3 rd ed, 2015 MM06-A2: Quantitative Molecular Methods for Infectious Diseases, 2010 MM09: Nucleic Acid Sequencing Mrthods in Diagnostic Medicine, 2 nd ed, 2014 MM13-A: Collection, Transport, Preparation, and Storage of Specimens for Molecular Methods, 2005 MM14-A2: Design of Molecular Proficiency Testing/External Quality Assissment, 2 nd ed MM17-A: Verification and Validation of Multiplex Nucleic Acid Assays, 2008 MM19-A: Establishing Molecular Testing in Clinical Laboratory Environments, 2011 MM13AQG: Handling, Transport, and Storage of Specimens for Molecular Methods Quick Guide

53 CLSI Reference Documents C24-A3: Statistical Quality Control for Quantitative Measurements: Principles and Definitions, 4 th ed, 2016 EP05-A3: Evaluation of Precision Performance of Quantitative Measurement Procedures, 2014 EP6-A: Evaluation of the Linearity of Quantitative Measurement Procedures: A Statistical Approach, 2003 EP09-A3: Measurement Procedure Comparison and Bias Estimation Using Patient Samples, 3 rd ed, 2013 EP12-A2: User Protocol for Evaluation of Qualitative Test Performance, 2008 EP14-A3: Evaluation of Commutability of Processed Samples, 3 rd ed, 2014 EP17-A2: Evaluation of Detection Capability for Clinical Laboratory Measurement Procedures, 2 nd ed, 2012

54 Reference Materials Burd, E.M Validation of Laboratory-Developed Molecular Assays for Infectious Diseases. Clin. Microbiol. Rev. 23: Jennings, L. et al Recommended principles and practices for validating clinical molecular pathology tests. Arch. Pathol. Lab. Med. 133: Cumitech 31A: Verification and Validation of Procedures in the Clinical Microbiology Laboratory, ASM Press, Bustin, S.A. et al The MIQE Guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55:

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