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Maintaining quality in molecular Diagnostics final layout
1.
2. Objectives
• Understand the need for a Quality System
in molecular diagnostics laboratories
• Understand the major components of a
QS
• Understand the deliverables of QS in
molecular diagnostics
3.
4. Available Genetic Tests and Laboratories Performing
Molecular Genetic Tests
Data source: GeneTests database /
www.genetests.org
5.
6. Practical Applications of Molecular
Diagnostics
Detection, quantitation, genotyping of infectious agents
Viruses, bacteria, fungi, and parasites
Detection of defective genes and variations in the genome
o Molecular genetics: Genetic disorders (neuromuscular, endocrine,
cardiovascular, etc., diagnosis of existing disease or predisposition)
o Molecular oncology: Hematological malignancies, and gene defects,
expression profiles, etc., related to cancer
o Pharmacogenetics: Identification of metabolic gene variants (slow,
average, fast metabolizers, non-responders) to optimize drug therapy
o Genomics: Uses genomic information (gene expression and gene pattern)
for disease susceptibility, diagnostic classification, prognosis, and optimal
therapy
Identification and characterization of individuals
Paternity, forensic medicine, pathology, transplantation
7. Special considerations for
molecular diagnostics laboratories
Clinical validity and utility of nucleic acid tests
Providing clinical interpretation of test results
Staffing and technical expertise
Regulatory oversight and best practice
considerations
9. Establishment of performance specifications
Accuracy
Precision
Analytic sensitivity
Analytic specificity, to include interfering substances
Reportable range of test results
Reference intervals or normal values (if applicable)
For quantitative assays:
Linearity
Dynamic range
Limit or Detection (LOD)
Lowest Limit of Quantitation (LLOQ)
For genetic tests: establish clinical usefulness and validity,
including clinical sensitivity and specificity, and positive and
negative predictive value
10. If the test is a lab-developed human
genetic test
Conduct a review of available scientific studies and
pertinent references
Define appropriate patient populations for which the
test should be performed
Select the appropriate test methodology for the
disease or condition being evaluated
Establish analytic performance specifications and
determine quality-control procedures using the
appropriate number, type, and variety of samples
Ensure that test results can be interpreted for an
individual patient or family and that the limitations of
the test are well defined and reported
11. Specimen selection for test validation
Evaluate the adequacy of the specimens for the
prevalence of the disease and the mutations or
variants
Specimen types may include blood, buccal swabs,
dried blood spots, fresh or frozen tissue, paraffin-
embedded tissue, or prenatal specimens
For a multiplex genetic test, all the mutations or
variants to be detected should be included in
performance establishment
For rare genotypes/mutations, alternative samples
acceptable
Specimen selection for test validation
12. Documentation of data
o Completeness
o Consistency
o Accuracy
o Reconstructability
“All data generated during the conduct of a study, except those that are
generated by automated data collection systems, shall be recorded
directly, promptly, and legibly in ink. All data entries shall be dated on
the date of entry and signed or initialed by the person entering the data.
Raw data includes the worksheets, calibration information, records and
notes of original observations, and activities of a study that are
necessary for the reconstruction and evaluation of the study. May
include photographic materials, computer printouts, automated and
hand recorded datasheets.”
FDA Good Laboratory Practices
13. 100
1,000,000
100,000
10,000
1000
10
1 2 3 4 5 6
Defectspermillion
Sigma Scale of measure
Domestic airline Fatality
rate
IRS Tax advice
(Phone In)
Order write up
Doctor prescription writing
Restaurant Bills
Airline Baggage
Handling
Laboratory Errors
Plebani M. The detection and prevention of errors in laboratory
medicine.
Ann Clin Biochem. 2010 Mar;47(Pt 2):101-10.
1
14. Background
1. Global Increase in Molecular Genetic Testing Applications
1. International Strides for Improving Quality Management in Genetic Testing services
A. OECD Guidelines for Quality Assurance in Molecular Genetic Testing. Organisation for
Economic Co‐operation and Development (OECD); 2007
B. EuroGentest – Harmonizing genetic testing across Europe
C. International Organization for Standardization (ISO) 15189 (2012). Medical laboratories
requirements for quality and competence
D. Increasing adherence to ISO and other national/international quality standards (eg,
countries in Europe, Asia, Americas, other continents)
3. CLSI Standards
A. Quality management systems (QMS) guidelines (eg, GP26‐A4)
B. Molecular methods guidelines (heritable diseases and oncology, molecular
hematopathology, FISH, infectious diseases, new test implementation, etc.)
C. Before MM20: No CLSI document specifically addressed QMS implementation and
maintenance in molecular genetic testing
15.
16. What is the
Organization for Economic Cooperation and Development?
(OECD)
• Governmental Organization - established in 1961.
• Origin traced to post-WWII Marshal Plan
• 30 member countries + cooperative arrangements with 70+
others
• Focus is to promote economic growth and financial stability
• Biotechnology and health care viewed as key sectors
• Molecular genetic testing viewed as important and evolving
• Lack of an international framework
http://www.oecd.org
17. The Journey to Guideline Development
Focus: Molecular genetic testing for medical (disease-related) conditions
2000
2005
2007
18. Variables associated with higher quality indices
1. Standard Operating Procedures exist
2. Standard operating procedures are reviewed by director
3. Laboratory test result report is issued (written or electronic)
4. Laboratory test result report is reviewed by director
5. Offering of prenatal / pre-implantation testing
6. Affiliation with a genetics unit
7. Licensing and accreditation
8. Participation in proficiency testing
9. Not primarily in a research setting
10. Maintaining data on turnaround time
11. Lab director has an MD or PhD
12. Lab director is certified
13. Lab director has formal training
14. Lab technicians have a university degree
15. Lab technicians have relevant training
19. OECD Guidelines for Quality Assurance
in Molecular Genetic Testing
Promote minimum standards
Facilitate mutual recognition of quality assurance
frameworks
Strengthen international co-operation to facilitate cross-
border flow of patient specimens for medically necessary
testing
Increase public confidence in the governance of
molecular genetic testing
20. OECD Guidelines for Quality Assurance
in Molecular Genetic Testing
Components
1. General principles and best practices
2. Quality assurance systems
3. Proficiency testing
4. Quality of result reporting
5. Education and training standards
6. Annotations
Organization:
Principles (1,2,3...): Primarily directed to governments
Best Practices (i, ii, iii): Primarily directed to laboratories and other entities
21. General principles and best practices
A.2 - Molecular genetic testing should be delivered within the
framework of healthcare.
A.i - Regulatory/professional bodies should, as appropriate, review
whether instruments available to manage a quality assurance
framework require adaptation for molecular genetic testing
A.3 - All molecular genetic testing services should be provided and
practices under a quality assurance framework
A.iii - Molecular genetic test results should be reported back to the
referring health care professional to enable counseling and healthcare
decision making
22. Quality Assurance Systems
in Molecular Genetic Testing
B.1 - Governments and regulatory bodies should recognize that
accreditation of medical laboratories is an effective procedure
for assuring quality.
B.i. - All laboratories reporting molecular genetic testing results
for clinical care purposes should be accredited or hold an
equivalent recognition. (additional clarification for role
of research laboratories)
B.9 - Governments should encourage international collaboration
for the development and validation of molecular genetic tests.
B.viii - Laboratories should cooperate (internationally) to collect,
develop, verify and make available reference materials
23. Proficiency Testing:
Monitoring the Quality of Laboratory
Performance
C.1 - The performance of laboratories offering clinical molecular genetic
tests should be measured.
C.iii - Proficiency testing schemes should be structured to assess all
phases of the laboratory process, including result reporting.
C.4 - Accreditation or equivalent recognition should be the basis for the
international recognition of proficiency testing scheme and providers.
C.v - Laboratories should participate in a proficiency testing scheme for
every test offered, when such schemes exist. When not available, they
should participate in alternate methods.
24. Quality of Result Reporting
D.1 - All laboratories should issue molecular genetic testing
results in the form of a written and/or electronic report to the
referring health professional
D.i - Reports should communicate information effectively taking
into account that the recipient may not be a specialist.
D.2 - Where reports are issued directly to patients, it should be
encouraged that laboratories recommend consultation with an
appropriate health care professional.
D.4 - The interpretation of the result should be appropriate to the
individual and clinical situation and based on objective evidence.
25. Education and Training
Standards for Laboratory Personnel
E.2 - Standards for laboratory accreditation or other equivalent
recognition should require that all molecular genetics
personnel have a combination of education, training, skills,
and experience that ensures their competence.
E.4 - Development of educational and training programmes
should be encouraged where they do not exist.
E.vi. Comparison of education and training systems between
jurisdictions should be facilitated as a means to establish
equivalence.
E.5 - Relevant government or professional authorities should
recognize medical genetics as a discipline comprising both a
clinical and a laboratory specialty.
26.
27.
28. Purposes of MM20
Provide guidance for implementing and maintaining
QMS in molecular genetic testing.
Address specific QMS challenges in technical processes
and laboratory/user interphases of molecular genetic
laboratory services.
Provide a resource to facilitate harmonized approaches
to accreditation to international laboratory standards.
29. What’s “Special” in MM20?
Extends international QMS standards/guidelines (eg, ISO 15189,
CLSI document GP26) into molecular genetic testing services
Incorporates recognized best practices for molecular genetic testing
worldwide
Follows new/extended path of workflow
Applies quality system essentials (QSEs) to quality management
and technical processes of molecular genetic testing
Features many tools, job aids, resources
30. Scope
Guidance for Implementing and Maintaining QMS for
Nucleic Acid–Based Human Molecular Genetic Testing
1. Intended for heritable (including pharmacogenetic testing) and
acquired conditions (eg, molecular oncology testing)
2. Not intended to address molecular infectious disease testing,
biochemical genetic testing, cytogenetic testing, specific technical
processes of molecular cytogenetic testing, molecular testing for
nonclinical purposes, or direct‐to‐consumer laboratory services
Concordant with Use of ISO QMS Standards and Other
CLSI Guidelines (eg, GP26, MM01, MM12, MM17,
MM19)
32. Need for Specific Quality
Management System
Guidance
Quality Laboratory Services
1. Most appropriate examination procedures
2. Best suited sample(s)
3. Accurate and timely results with proper interpretation
4. Accurate and timely communications
Quality Management Challenges for Molecular Genetic Testing
1. Diverse spectrum of testing services
2. Expanding applications impacting all medical disciplines
3. New users and clients continuously faced by laboratories
4. Laboratory’s continuing need to‐
• Consider new examination methods/procedures.
• Update existing examination procedures.
• Ensure effective communications with users and clients.
Prerequisites for Providing Testing Services
1. Planning and preparation activities to ensure QMS/readiness for introducing or providing
molecular genetic testing services
2. Validation/verification of new or updated examination procedures before receiving test
requests/testing patient samples
35. Quality System
Essentials for Molecular
Genetic Testing
Discuss implementation of 12 QSEs in molecular genetic testing services (Section 6
in MM20).
6.1 Organization
6.2 Personnel
6.3 Documents and Records
6.4 Advisory Services
6.5 Assessment
6.6 Management of Nonconforming Events
6.7 Information Management
6.8 Continual Improvement
6.9 Use of Referral Laboratories
6.10 Evaluation of Vendor Qualification
6.11 Laboratory Equipment
6.12 Facilities, Environment, and Safety
Describe policies and procedures to specifically address QMS needs in providing
molecular genetic testing services.
36.
37. Example: Quality System
Essential Assessment
Quality Indicators (QIs) – providing examples in the
laboratory’s path of workflow
Internal Audits
1. Horizontal – for general processes in the path of workflow
(eg, acceptance of sequencing reactions)
2. Vertical – for a specific laboratory process (eg,following a
sample from sample receipt to result reporting)
External Assessment
1. Voluntary and mandatory
2. Accreditation vs (third‐party) certification
Management Review
38.
39. Example: Quality System
Essential Information
Management
Laboratory Information Systems (LIS) Considerations
1. Direct interface/compatibility with electronic medical records (for test ordering and
reporting)
2. Patient information (eg, race/ethnicity, indication for testing, family history) collected and
directly entered with test requests
3. Accommodating all fields/elements of molecular genetic test reports
4. Monitoring examination procedures, quality control (QC) tracking, follow‐up on TAT
Accessibility and Retrievability
Confidentiality and Security
Data Management
1. Maintaining databases of sequence variants (eg, sequence variants identified in the
laboratory and literature, reference sequences, disease‐specific mutation databases)
2. Monitoring/updating as variants are reclassified
3. Ensuring consistency of result interpretation
40. Path of Workflow –
Technical Processes
Planning and Preparation
Validation/Verification of Test Performance
Processes for providing examination services to
laboratory users
1. Preexamination activities
2. Examination activities
3. Postexamination activities
41. Planning and Preparation
Fundamental Management Considerations for Providing Molecular Genetic Test Services
Ensuring all QSEs are in place and adequate for new tests/test services
Determining preparedness for all applicable requirements
Determining needs and demands, benefits and costs
Identifying personnel competencies, training needs, and responsibilities
Identifying special issues
Informed consent
a) Genetic counseling
b) Intellectual property/licensing concerns
c) Ethical issues (testing of minors, use of tested samples, confidentiality)
42. Technical Aspects to Consider
Specific intended use (and examination method to be used), different
planning issues:
a) Diagnostic testing
b) Carrier testing
c) Presymptomatic testing
d) Prenatal diagnosis
Documenting clinical validity and utility:
a) Indications
b) Contraindications
Planning for validation/verification of test performance
43. Validation/Verification of
Test Performance
Develop validation/verification procedures
1. The intended use of the test (eg, carrier testing, fetal testing,
diagnostic testing)
2. Target genes, sequences, mutations
3. Expected patient population
4. Test methods to be compared or the method of choice to be
used
5. Type(s) of samples to be used
6. Analytical performance characteristics to be determined
7. Sources of reference materials
8. How performance specifications will be analyzed
9. How test limitations should be defined (eg, rate of allele
drop‐out, interfering mutations, polymorphisms)
10. Corrective actions when problems occur
44. Identify samples/materials for analytical validation/verification
1. Adequate number, type, and variety of samples for establishing
test performance specifications and defining limitations
2. Control materials, calibration materials, other reference materials
Determine analytical performance characteristics; define
performance specifications and limitations.
Document results/findings.
Prepare operational procedures for examination of patient samples.
Perform ongoing validation.
45. Pre-examination Activities
Begin with the laboratory informing users about:
① The molecular genetic tests it performs
② Test selection
③ Patient preparation (if needed)
④ Sample collection, handling, transport, submission with test requisitions (eg, sample
collection/submission manual)
Information provided by laboratory aids health care providers and other users
in:
① Considering indications for testing/recognizing the need for a genetic test
② Selecting indicated test(s)
③ Shared decision making between a health care provider and the patient/pretest
genetic counseling leading to informed consent as indicated
④ Sending test request with patient sample(s) to laboratory
Advisory services regarding consideration/selection of genetic tests
Test referring process in case of sample referral
46.
47.
48. Examination Activities
Examination Activities
I. Selection of test procedures according to user needs/expectations
II. Sample preparation/processing (eg, nucleic acid extraction/purification)
III. Examination procedures
IV. QC procedures
V. Documentation of test results and findings
QC Plan/Program
I. Describe how all steps of analytical examination procedures are monitored.
II. Essential elements:
Types of controls/control materials
Frequency and placement of controls
Analysis and recording of QC results
Pass/fail criteria
Corrective and preventive actions
Alternative control procedures when control materials are not available
49.
50. Postexamination Activities
Postexamination Activities
Reviewing examination results
Providing laboratory interpretation
Generating examination reports
Transmitting test reports to the test requestor or other clinical users
Providing laboratory consultation regarding test results, result interpretation, follow‐up
examinations or services
Archiving of examination records, reports, and tested patient samples
Recommended Contents of Molecular Genetic Test Reports
Procedures for Releasing/Reporting Test Results
Who may release test results and to whom
Maintaining confidentiality of patient/family information
Monitoring accidental disclosure and documenting corrective actions
Procedures for Corrected, Revised, Amended Reports
51.
52. Ensuring Quality of
Patient Testing
Proficiency Testing/External Quality Assessment (PT/EQA)
Existing programs for commonly performed molecular genetic tests (eg, CAP, CF
[European] Network, EMQN, EuroGentest, UK NEQAS)
Differences between PT/EQA samples and actual patient samples: greater benefits
from challenging more steps of the testing process
Section 7.3.3 in MM20 and CLSI documents GP27, MM01, MM14, and MM19
Alternative Performance Assessment
Interlaboratory comparison and intralaboratory evaluation when sample exchange is
not Available
As frequent as would be required by participation in formal PT/EQA
Rigorous in review and interpretation of results
Management of Performance Assessment Results
Important part of the laboratory’s quality assurance plan
Documentation of assessment, results, and corrective actions
Written policies on review and retention of performance assessment results
54. Personnel Competency
Assessment
Methods for Competency Assessment for Laboratory
Management
Appropriate levels of continuing education units
Peer‐reviewed journal articles studied
Membership/participation in professional organizations
Credentials and maintenance of certification activities
Proficiency slides or samples examined
Interlaboratory sample exchanges with interpretation
Assessment at annual review or other time, documented with
appropriate form
Personnel competency assessment for testing personnel
Determining when competency assessment is needed
Key elements of competency assessment program for testing
personnel