2018 focus on compliance - college of american...
TRANSCRIPT
2018 Focus on Compliance
Karl Voelkerding, MD, FCAP Birgit Funke, PhD, FACMG Avni Santani, PhD, FACMG
September 12, 2018
Next Generation Sequencing: What Does Compliance Look Like?
Disclosure
© 2018 College of American Pathologists. All rights reserved.
The following authors/planners/reviewers have financial interests/ relationships to disclose:
Andrew Goodwin, MD, FCAP
Haematologic Technologies
Medical Director Monetary stipend
Lee Hilborne, MD, MPH, DLM(ASCP) Avni Santani, PhD, ABMGG Karl Voelkerding, MD, FCAP
Quest Diagnostics CHOP Veritas Agilent PierianDx
Employee Consultant Consultant License agreement Scientific advisor
Compensation, stock Consulting fee Consulting fee Fees Consulting fee
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Disclosure, cont’d.
© 2018 College of American Pathologists. All rights reserved.
Birgit Funke, PhD, ABMGG, ACMG
Michael Talbert, MD
Gregory Gagnon, MD, FCAP
Carlos Machicao, MD, FCAP
S. Robert Freedman, MD, FCAP
Jacob Mayer, Jr PhD, HCLD
Kenneth Klein, MD, FCAP
Justin Rueckert, DO, MLS(ASCP)cm
Ritu Nayar, MD, MBBS, FCAP Marian Briggs, MS, MT(ASCP)
The following authors/planners/reviewers have no financial interests/relationships to disclose:
3
Accreditation The College of American Pathologists (CAP) is accredited by the Accreditation Council for Continuing Medical Education (ACCME) to provide continuing medical education for physicians.
CE (CONTINUING EDUCATION FOR NON-PHYSICIANS) The CAP designates this educational activity for a maximum of 1 credit/hour of continuing education. Each participant should only claim those credits/hours he/she actually spent in the activity.
ASCP STATEMENT The American Society for Clinical Pathology (ASCP) Board of Certification (BOC) Certification Maintenance Program (CMP) accepts this activity to meet the continuing education requirements.
CALIFORNIA AND FLORIDA STATEMENT This activity is approved for continuing education credit in the states of California and Florida.
© 2018 College of American Pathologists. All rights reserved. 4
Today’s Presenter Karl Voelkerding, MD, FCAP
Dr. Voelkerding is a professor of pathology at the University of Utah School of Medicine and past president of the Association for Molecular Pathology. He is the former chair of the College of American Pathologists’ Next-Generation Sequencing Project Team, which developed laboratory accreditation requirements and proficiency testing programs for clinical next-generation sequencing. Dr. Voelkerding is currently chair of the College of American Pathologists’ Genomic Medicine Resource Committee. Dr. Voelkerding received his MD from the University of Cincinnati College of Medicine and is board certified in clinical pathology and molecular genetic pathology. His research focuses on the translation of genomics technologies into clinical diagnostics.
© 2018 College of American Pathologists. All rights reserved. 5
Today’s Presenter
© 2018 College of American Pathologists. All rights reserved.
Birgit Funke, PhD, FACMG • Associate Professor of Pathology
(part-time), Harvard Medical School • Vice President of Clinical Affairs,
Veritas Genetics
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Today’s Presenter Avni Santani, PhD, FACMG
• Director - Clinical Laboratories, Strategic Partnerships and Innovation
• Director - Center for Applied Genomics, The Children’s Hospital Of Philadelphia
• Associate Professor of Clinical Pathology & Lab Medicine
• Education - Perelman School of Medicine, University of Pennsylvania
© 2018 College of American Pathologists. All rights reserved. 7
Objectives
• Explain the accreditation requirements for Next Generation Sequencing (NGS)
• Describe practical steps to ensure appropriate implementation of NGS testing
• Demonstrate compliance with the accreditation requirements
© 2018 College of American Pathologists. All rights reserved. 8
• First Published in the 2012 edition of the Molecular Pathology Checklist
• Revised Yearly as NGS Clinical Testing Has Advanced
CAP NGS Laboratory Accreditation Requirements
© 2018 College of American Pathologists. All rights reserved. 9
• Guiding Principle – Finding the Right Balance
• Foster Innovation and Technology Adoption – Assure Patient Safety
CAP NGS Laboratory Accreditation Requirements
© 2018 College of American Pathologists. All rights reserved. 10
Wet Bench Process • Sample Handling
• Library Preparation • Sequence Generation
Bioinformatics “Dry Bench” Process • Sequence Alignment to Reference
• Variant Identification • Variant Annotation (eg CFTR
p.Arg205Lys)
Data Interpretation and Reporting
Medical Practice
FASTQ File
Annotated Variants
Analytical
Laboratory Process
CAP Definition of a NGS Test
© 2018 College of American Pathologists. All rights reserved. 11
Majority of Laboratories Perform NGS Testing
In One Primary Physical Laboratory
Wet Bench Process Sequencing
Bioinformatics Process
Interpretation and Reporting
Single CLIA License
Data Integrity Security Privacy
© 2018 College of American Pathologists. All rights reserved. 12
Some Laboratories Outsource Individual Process Steps
Wet Bench Process Sequencing
Bioinformatics Process
Interpretation Reporting
Primary Laboratory
Reference Laboratory
Primary Lab Receives Patient Sample
Outsource
© 2018 College of American Pathologists. All rights reserved. 13
Some Laboratories Outsource Individual Process Steps
Interpretation Reporting
Primary Laboratory
Reference Laboratory
Primary Lab Receives Patient Sample
Outsource
Wet Bench Process Sequencing
Bioinformatics Process
© 2018 College of American Pathologists. All rights reserved. 14
• Written to Accommodate Diversity of Testing Configurations
• Single Laboratory to Primary and Reference Laboratory
CAP NGS Laboratory Accreditation Requirements
© 2018 College of American Pathologists. All rights reserved.
Diversity
15
Some Laboratories Outsource Individual Process Steps
Wet Bench Process Sequencing
Bioinformatics Process
Interpretation Reporting
Primary Laboratory
Reference Laboratory
Primary Lab Receives Patient Sample
Outsource
“Distributive” Testing Model Concept
CAP Requires Integrated Methods Based Validation © 2018 College of American Pathologists. All rights reserved. 16
Some Laboratories Outsource Individual Process Steps
Interpretation Reporting
Primary Laboratory
Reference Laboratory
Primary Lab Receives Patient Sample
Outsource
Wet Bench Process Sequencing
Bioinformatics Process
“Distributive” Testing Model Concept
CAP Requires Integrated Methods Based Validation © 2018 College of American Pathologists. All rights reserved. 17
Primary/Referring Laboratory
NGS Reference Lab
Policy
NGS Confirmatory Testing Policy
NGS Sample Provenance
Tracking
General
Exception Log/Record
Data Storage Local/Cloud
Data Transfer Confidentiality
Wet Bench
NGS Wet Bench Process
Documentation
NGS Wet Bench Process
Validation
Quality Management
Plan
Laboratory Records
Monitoring of Upgrades
Bioinformatics
NGS Bioinformatics
Pipeline Documentation
NGS Bioinformatics
Pipeline Validation
Quality Management
Plan
Pipeline Version Traceability
Monitoring of Upgrades
Interpretation
Sequence Variants
Interpretation and Reporting
Reporting of Incidental Genetic Findings
Current CAP NGS Laboratory Accreditation Requirements - 2018
© 2018 College of American Pathologists. All rights reserved. 18
Primary/Referring Laboratory
NGS Reference Lab
Policy
NGS Confirmatory Testing Policy
NGS Sample Provenance
Tracking
General
Exception Log/Record
Data Storage Local/Cloud
Data Transfer Confidentiality
Wet Bench
NGS Wet Bench Process
Documentation
NGS Wet Bench Process
Validation
Quality Management
Plan
Laboratory Records
Monitoring of Upgrades
Bioinformatics
NGS Bioinformatics
Pipeline Documentation
NGS Bioinformatics
Pipeline Validation
Quality Management
Plan
Pipeline Version Traceability
Monitoring of Upgrades
Interpretation
Sequence Variants
Interpretation and Reporting
Reporting of Incidental Genetic Findings
Current CAP NGS Laboratory Accreditation Requirements - 2018
© 2018 College of American Pathologists. All rights reserved. 19
Wet Bench Process • Sample Handling
• Library Preparation • Sequence Generation
Bioinformatics “Dry Bench” Process • Sequence Alignment to Reference
• Variant Identification • Variant Annotation (eg CFTR
p.Arg205Lys)
Data Interpretation and Reporting
FASTQ File
Annotated Variants
CAP Requires an Integrated Methods Based Validation
Integrated
Methods Based Validation
© 2018 College of American Pathologists. All rights reserved. 20
Wet Bench Process • Sample Handling
• Library Preparation • Sequence Generation
Bioinformatics “Dry Bench” Process • Sequence Alignment to Reference
• Variant Identification • Variant Annotation (eg CFTR
p.Arg205Lys)
Data Interpretation and Reporting
Integrated
Methods Based Validation
FASTQ File
Annotated Variants
Validation Specimens Contain a
Representative Spectrum of Variant
Types Test is Designed to Detect
Establish Assay Performance
CAP Requires an Integrated Methods Based Validation
© 2018 College of American Pathologists. All rights reserved. 21
NGS Test Validation – Choice of Specimens
Validation Specimens
Contain a Representative Spectrum of Variant Types Test is Designed to Detect
For Gene Panels Include Specimens that
Contain Common Mutations
(e.g. Cancer Hot Spots, CFTR p.Phe508del)
Methods Based
Gene or Analyte Based
Hybrid
CAP Requires an Integrated Methods Based Validation
Add Extra Specimens that Contain Variants That are Technically
Difficult to Detect
© 2018 College of American Pathologists. All rights reserved. 22
• We are sequencing every base instead of assaying known disease variants -- novel variant detection – Requires new validation approaches
– Methods–based validation
• The amount of data exceeds ability to process it manually – Increased reliance on computational resources and bioinformatics
• Changing role of laboratory director – Moving from predominantly technical focus to increasingly interpretive role
• Ability to sequence large numbers of genes – Increased burden on test content design
NGS has changed many things….
We need to develop new approaches and standards
© 2018 College of American Pathologists. All rights reserved. 23
Adapted from: Rehm et al. 2013
LIFECYCLE OF AN NGS BASED CLINICAL TEST
© 2018 College of American Pathologists. All rights reserved.
TARGET
CATPURE
TEST VALIDATION
LIBRARY PREP CAPTURE SEQ ANALYSIS
QUALITY MANAGEMENT
PATIENT TESTING
QC PT
GEN
E P
NL
- A
GEN
E P
NL
- B
GEN
E P
NL
- C
E X
O M
E
G E
N O
M E
P L A T F O R M (cumulative data)
Optimize components and entire test • General assay conditions • Coverage • Sample pooling • Analysis setting/thresholds Establish protocol for entire workflow
Validate entire test using set conditions • Sensitivity • Specificity • Robustness • Reproducibility Include samples representing • Different variant types (in/dels, substitutions, CNVs) • Disease specific aspects (common pathogenic variants)
TEST OPTIMIZATION
Quality Control (QC) • Every run
Proficiency Testing (PT) • Periodically
TEST DESIGN
Technical design
Content design
Added dimension Greatly increased complexity
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A GROWING LIST OF PROFESSIONAL NGS GUIDELINES
Organization/Entity PMID Year Title
CDC 23138292 2012 Assuring the quality of next-generation sequencing in clinical laboratory practice.
CDC 26154004 2015 Good laboratory practice for clinical next-generation sequencing informatics pipelines.
ACMG 23887774 2013 ACMG clinical laboratory standards for next-generation sequencing.
ACMG/AMP 25741868 2015
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
AMP/CAP 28341590 2017
Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.
AMP/CAP 29154853 2018
Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.
CAP 25152313 2015 College of American Pathologists' laboratory standards for next-generation sequencing clinical tests.
CAP 28322587 2017 Development and Validation of Targeted Next-Generation Sequencing Panels for Detection of Germline Variants in Inherited Diseases.
CAP 28362156 2017 Development and Validation of Clinical Whole-Exome and Whole-Genome Sequencing for Detection of Germline Variants in Inherited Disease.
CLSI N/A 2014 MM09: Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine, 2nd Edition
New York State N/A 2015 Guidelines for Validation Submissions of Next Generation Sequencing (NGS) assays under the NYS Testing Category of Genetic Testing– Molecular
FDA N/A 2016 Use of Standards in FDA Regulatory Oversight of Next Generation Sequencing (NGS)-Based In Vitro diagnostics (IVDs) Used for Diagnosing Germline Diseases
Santani et al. 2018 (manuscript under review, JMD) © 2018 College of American Pathologists. All rights reserved. 25
THERE IS A NEED FOR MORE….
….. concrete guidance • Labs want to do the right thing but it’s not easy to
translate recommendations into an SOP for how to set up high quality NGS testing
• Need step by step instructions that “get into the weeds”
© 2018 College of American Pathologists. All rights reserved. 26
© 2018 College of American Pathologists. All rights reserved.
THE CAP CHECKLIST HAS TRIED TO ACCOMMODATE THIS NEED
From the 2017 CAP checklist:
This is a SINGLE requirement
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EVOLUTION OF THE CAP NGS CHEKLIST (MOL.36010 – Analytical Wet Bench Process Documentation)
© 2018 College of American Pathologists. All rights reserved.
2013 2015
The complexity of NGS is not compatible with what the checklist was designed for
2017
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© 2018 College of American Pathologists. All rights reserved.
**REVISED** 08/21/2017 MOL.36015 NGS Analytical Wet Bench Process Validation Phase II The laboratory validates the analytical wet bench process and revalidates the entire process and/or confirms that the performance of the components of the process is acceptable when modifications are made. NOTE: The output of the NGS analytical wet bench process is a collection of sequence data that requires additional bioinformatics processing and analysis to determine whether the sequence is of sufficient quality and quantity for the intended test. To determine this, and to ensure acceptable beginning-to-end test performance, validation of the NGS analytical wet bench process must be integrated with the bioinformatics process validation for the intended test (see MOL.36115). The analytical wet bench process and the bioinformatics process for a test may occur within a single laboratory, or in a combination of primary and referral laboratories (see MOL.35840). Whether performed in a single laboratory, or in a distributive model involving primary and referral laboratories, the validations of the wet bench and bioinformatics processes for an intended test must be integrated to ensure acceptable beginning-to-end test performance. It is the responsibility of the laboratory director or designee meeting CAP director qualifications to review and approve all validations relevant to the intended test for processes performed within their laboratory, and to review all validations relevant to the intended test for processes performed in referral laboratories, if applicable. Laboratories validating NGS tests must comply with MOL.31015 and/or MIC.64770, as applicable, and meet the requirement that validations are performed with samples for each type of specimen expected for the assay (e.g. blood, fresh/frozen tissue, paraffin embedded tissue, prenatal specimens, saliva, culture isolates). Validations can be augmented by, but not supplanted with, additional reference standards (e.g. cell lines such as NIST NA12878). • Analytical validations must consist of a baseline methods-based validation that establishes the test's general
performance for the detection of the sequence variant type(s) that the test is designed to identify. For tests that are offered for specific clinical indications (e.g. diagnostic gene panels) the laboratory should investigate whether any analyte, disease or gene specific needs exist that necessitate inclusion of additional specimens or reference samples in the validation. For example, this may include samples containing prevalent pathogenic variants, especially if they are technically difficult to accurately detect (e.g. large indels). For detailed requirements on validation see MOL.36115 (NGS Analytical Bioinformatics Process Validation).
“…I understand what a methods-based validation approach is - but how exactly do I go about this?”
YET….WE ARE DEFINING MOSTLY WHAT NEEDS TO BE DONE, BUT NOT HOW…
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A “COMPANION RESOURCE” FOR THE CAP CHECKLIST
Manuscript in revision at the Journal of Molecular Diagnostics
© 2018 College of American Pathologists. All rights reserved. 30
FILLABLE WORKBOOKS THAT GUIDE THE WAY THROUGH THE NGS TEST LIFECYCLE
© 2018 College of American Pathologists. All rights reserved. 31
TEST DESIGN
© 2018 College of American Pathologists. All rights reserved.
Background Detailed Instructions 32
© 2018 College of American Pathologists. All rights reserved.
This information is critical for appropriate test design, examples: - CNVs rare: supplemental assay less important - Gene not well associated with disease –careful when including
into gene panel !
Goal: ensure both clinical and technical validity
TEST DESIGN
33
© 2018 College of American Pathologists. All rights reserved.
Now you’ve chosen your genes – preparing for technical design
TEST DESIGN
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© 2018 College of American Pathologists. All rights reserved.
TEST VALIDATION
35
© 2018 College of American Pathologists. All rights reserved.
Formulas to help translate
Helpful comments and concrete examples
Common sense translation
TEST VALIDATION
36
© 2018 College of American Pathologists. All rights reserved.
TEST VALIDATION
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© 2018 College of American Pathologists. All rights reserved.
TEST VALIDATION
• Build your validation runs • Start with assembling sample list • Annotate with pertinent information
- Which validation “layer” is served by the sample - Specific variants of interest present? - Which metric is served (intra/inter-run variability)
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© 2018 College of American Pathologists. All rights reserved.
• Place samples on a run grid • Example here:
• HiSeq 2500 • 10 samples/lane • Run 1: Same libraries run 3X • Run 2+3: New libraries of same samples
TEST VALIDATION
39
© 2018 College of American Pathologists. All rights reserved.
METHODS-BASED TEST VALIDATION -PERFORMANCE METRICS SUMMARY
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NEXT STEPS? Short Term • Make worksheets publicly available • Invite comment from users (public access, CAP
website) • Adapt to incorporate other applications (somatic
NGS)
Medium Term: Make it a “living document” • Iterate on first version based on user feedback and
evolving evolution of NGS
Long Term • Convert to web based application
© 2018 College of American Pathologists. All rights reserved. 41
Demonstrate Compliance with the Accreditation Requirements
• Preparing for an inspection of an NGS laboratory
• Integrated inspection (MOL, COM, GEN, TLC)
- Refer to latest checklist edition • The highlights of NGS section of the MOL
Checklist will be covered • This webinar is not a substitute for the
comprehensive CAP Checklists
© 2018 College of American Pathologists. All rights reserved. 42
PREPARATION
Think like an Inspector!
© 2018 College of American Pathologists. All rights reserved. 43
Review the Checklists
• New or revised questions? • Requirement AND NOTES are applicable • Evidence of Compliance suggests ways to
ensure compliance • Review R.O.A.D instructions to inspector;
documents and records must be available • Is the available documentation acceptable to
you if you were the inspector?
© 2018 College of American Pathologists. All rights reserved. 44
• High volume tests • Low volume tests • High patient impact tests • Tests from variant PT report • Concerns from previous deficiencies • New analyte, new instrument
Most Likely Choices During an Inspection
© 2018 College of American Pathologists. All rights reserved. 45
© 2018 College of American Pathologists. All rights reserved. 46
Top Molecular Deficiencies
MOL.30785 For each test there is a validation summary addressing analytical and clinical performance parameters.
MOL.34495 Quality control data are reviewed and assessed at least monthly by the laboratory director or designee
MOL.49570 The final report includes an appropriate summary of the methods, the loci or variants tested and the analytic interpretation. When appropriate, the final report includes the clinical interpretation.
MOL.35350 Nucleic acid amplification procedures (e.g. PCR) are designed to minimize carryover (false positive results) using appropriate physical containment and procedural controls.
MOL.34229 For qualitative tests, positive, negative and sensitivity controls are included for each assay, when appropriate, in every run and as specified in the manufacturer's instructions (as applicable) and laboratory procedure.
© 2018 College of American Pathologists. All rights reserved. 47
MOL.36105 The laboratory has a written procedure that describes the steps included in recording the bioinformatics process used to analyze, interpret, and report NGS test results.
MOL.36115 The laboratory validates the analytical bioinformatics process (also termed pipeline) and revalidates the entire process and/or confirms the performance of the components of the process as acceptable when modifications are made.
MOL.31145 The results of each validation study include a sufficient number of samples with repeated analyses to provide a high degree of assurance of the test's precision or reproducibility
MOL.34352 The results of controls are reviewed for acceptability before reporting of results.
MOL.36010 The laboratory has a written procedure for performing the analytical wet bench process used to generate next generation sequencing data.
Top Molecular Deficiencies cont.
© 2018 College of American Pathologists. All rights reserved. 48
© 2018 College of American Pathologists. All rights reserved. 49
Primary/Referring Laboratory
NGS Reference Lab
Policy
NGS Confirmatory Testing Policy
NGS Sample Provenance
Tracking
General
Exception Log/Record
Data Storage Local/Cloud
Data Transfer Confidentiality
Wet Bench
NGS Wet Bench Process Documentation
NGS Wet Bench Process
Validation
Quality Management
Plan
Laboratory Records
Monitoring of Upgrades
Bioinformatics
NGS Bioinformatics
Pipeline Documentation
NGS Bioinformatics
Pipeline Validation
Quality Management
Plan
Pipeline Version
Traceability
Monitoring of Upgrades
Interpretation
Sequence Variants
Interpretation and Reporting
Reporting of Incidental Genetic Findings
Current CAP NGS Laboratory Accreditation Requirements - 2018
Demonstrating Compliance • Reference Laboratory: Records of evaluations of referral
laboratories for NGS referral testing and copies of valid CLIA and/or CAP certificates
• Specimen Provenance: Specimen handling, chain of custody and data transfer starting from initial NGS test order to the final report
• Confirmatory Studies: Determine during validation if and when confirmatory testing of NGS identified variants should be performed
• If certain variants are NOT confirmed, then provide rationale for, and data supporting the rationale
• Records of review of correlation of NGS test results and confirmatory test results over time
© 2018 College of American Pathologists. All rights reserved. 50
© 2018 College of American Pathologists. All rights reserved. 51
Current CAP NGS Laboratory Accreditation Requirements - 2018
Primary/Referring Laboratory
NGS Reference Lab
Policy
NGS Confirmatory Testing Policy
NGS Sample Provenance
Tracking
General
Exception Log/Record
Data Storage Local/Cloud
Data Transfer Confidentiality
Wet Bench
NGS Wet Bench Process Documentation
NGS Wet Bench Process
Validation
Quality Management
Plan
Laboratory Records
Monitoring of Upgrades
Bioinformatics
NGS Bioinformatics
Pipeline Documentation
NGS Bioinformatics
Pipeline Validation
Quality Management
Plan
Pipeline Version
Traceability
Monitoring of Upgrades
Interpretation
Sequence Variants
Interpretation and Reporting
Reporting of Incidental Genetic Findings
Demonstrating Compliance cont. • Review of exception log and corrective action • Data Security: records of policies and protocols to ensure
patient confidentiality, security and data integrity • Encryption, control of physical and virtual access to data,
system backups and redundancy • Records of audit trails and copies of HIPAA Associate
Agreements • Data Storage: Policy must be in accordance with local, state
and federal requirements for storage of data • Written policy that describes files, type of data to be
retained and length of retention
© 2018 College of American Pathologists. All rights reserved. 52
© 2018 College of American Pathologists. All rights reserved. 53
Current CAP NGS Laboratory Accreditation Requirements - 2018
Primary/Referring Laboratory
NGS Reference Lab
Policy
NGS Confirmatory Testing Policy
NGS Sample Provenance
Tracking
General
Exception Log/Record
Data Storage Local/Cloud
Data Transfer Confidentiality
Wet Bench
NGS Wet Bench Process
Documentation
NGS Wet Bench Process
Validation
Quality Management
Plan
Laboratory Records
Monitoring of Upgrades
Bioinformatics
NGS Bioinformatics
Pipeline Documentation
NGS Bioinformatics
Pipeline Validation
Quality Management
Plan
Pipeline Version Traceability
Monitoring of Upgrades
Interpretation
Sequence Variants
Interpretation and Reporting
Reporting of Incidental Genetic Findings
Demonstrating Compliance cont.
• Review all centrally located records • Review documentation of maintenance, reagent labeling,
testing performed, QC, and results reporting • Ensure that policies and procedures are available to testing
personnel
© 2018 College of American Pathologists. All rights reserved.
54
Demonstrating Compliance cont. • Monitoring of Proficiency Testing (PT)
– Required for all analytes regardless of CLIA complexity classification
– PT must be specific to the analyte and system matrix – If PT is not available, another mechanism must be
defined to assess accuracy and reliability of the system (alternative assessment)
– PT must be performed by, and rotated among, the same individuals who perform the routine testing
– Corrective action must be documented and reviewed for unacceptable results and for ungraded results
© 2018 College of American Pathologists. All rights reserved. 55
Demonstrating Compliance cont. • Quality Control
– QC must be verified prior to reporting patient results – Corrective action must be documented and reviewed – QC must be handled in the same manner as patient
samples and performed by those performing patient testing
© 2018 College of American Pathologists. All rights reserved. 56
Quality Control EXAMPLE CriteriaSpecimen quality Rejected and cancelled samples
Wrong sampleWrong type of tubeInsufficient quantityClottedMislabeled
Specimen cancellation Wrong testInsufficient specimenDegraded specimen
DNA quality OD 260/280 ratioOD 260/230 ratio
DNA quantification and integrity Gel electrophoresisSpectrophotometric Analysis
PRE-ANALYTIC QC FOR NGS - Examples
© 2018 College of American Pathologists. All rights reserved. 57
ANALYTIC QC FOR NGS - Examples Genomic DNA fragmentation Fragment size and distribution
Library preparationPre and post target enrichment size and concentration
Cluster Generation and Sequencing Cluster density and clusters passing filtersBase quality: Percentage of bases with Q>30 Error rate using Phi X-174 internal controlTotal reads passing filter
Sequence read alignment % Reads Aligned to Target% Reads Off target% of duplicated readsAverage Target CoverageDistribution of Coverage
Variant CallingAverage number of SNVs and indelsTransition to transversion ratio
Specimen verification
Specimen identity confirmation using independent genotyping approachSpecimen contamination identification
Variant confirmation by orthogona Rate of confirmation
© 2018 College of American Pathologists. All rights reserved. 58
POST-ANALYTIC QC FOR NGS - Examples
Case Statistics Average turnaround time
Test Specific ResultsNumber of positive and negative cases
Amended or corrected reports Number of clerical errorsChanges to variant classificationNumber of cases with changes to interpretation
© 2018 College of American Pathologists. All rights reserved. 59
© 2018 College of American Pathologists. All rights reserved. 60
Current CAP NGS Laboratory Accreditation Requirements - 2018
Primary/Referring Laboratory
NGS Reference Lab
Policy
NGS Confirmatory Testing Policy
NGS Sample Provenance
Tracking
General
Exception Log/Record
Data Storage Local/Cloud
Data Transfer Confidentiality
Wet Bench
NGS Wet Bench Process
Documentation
NGS Wet Bench Process
Validation
Quality Management
Plan
Laboratory Records
Monitoring of Upgrades
Bioinformatics
NGS Bioinformatics
Pipeline Documentation
NGS Bioinformatics
Pipeline Validation
Quality Management
Plan
Pipeline Version Traceability
Monitoring of Upgrades
Interpretation
Sequence Variants
Interpretation and Reporting
Reporting of Incidental Genetic Findings
Demonstrating Compliance cont. • Variant Interpretation: Provide validated algorithm for
classifying and interpreting variants • The ACMG guidelines for classification and
interpretation of germline variants in inherited disorders (Richards et al. 2015)
• Standard nomenclature (eg., HGVS and HUGO) – also consider: Infectious disease, somatic variants
• Incidental and Secondary findings: Describe approach for reporting findings unrelated to the clinical purpose of testing
© 2018 College of American Pathologists. All rights reserved. 61
College of American Pathologists (CAP) – led effort Creating practical, step-by-step guidance for
molecular laboratories Manuscript in revision at the Journal of Molecular Diagnostics
© 2018 College of American Pathologists. All rights reserved. 62
Remaining 2018 Focus on Compliance Webinars
© 2018 College of American Pathologists. All rights reserved. 63
© 2018 College of American Pathologists. All rights reserved.
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