CAP, AMP Release New Clinical Gene Panel Validation Guidelines; Also noted: New proposals for evidence levels in genome libraries

On March 23, 2017, CAP and AMP released a new, 25-page guideline to validation of next generation sequence panels.   The article, Jennings et al, has its journal home page here, PDF link here, and in the cloud, here.

For coverage at Genomeweb, here.

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Update December 2017:  Genomeweb article based on Ghosh et al., Genome Biology, on performance of algorithms relative to AMP guidance.  
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This is the fourth recent guidance for fundamental standards in next generation sequencing and data archiving.

See also Ritter et al. for guidelines on new standards for annotating and curating somatic tumor variants in libraries like ClinVar (here) and Li et al. on new standards for clinical reporting that is specific to somatic variants (here).  Li et al. note that most prior work has focused on clinical reporting of germline variants.   Finally, in May 2017, Strande et al. published guidelines for the firmness of validity or the evidence level of reported associations; this has relevance for both germline and tumor information archives; see Strande et al. here.

Though not related to somatic mutations, see also Richard et al., 2015, ACMG/AMP standards for reporting [germline] sequence variants (here), and a May 2017 paper by Invitae staff on SHERLOC, an interpretation system for germline variants (Nykamp et al., here) which is asserted to refine some ambiguities in AMP guidelines.

Abstract of Jennings et al. clipped after the break.

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

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

Jennings LJ et al. 

DOI: http://dx.doi.org/10.1016/j.jmoldx.2017.01.011

Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists.

These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics. 

The recommendations emphasize the role of laboratory director in using an error-based approach that identifies potential sources of errors that may occur throughout the analytical process and addressing these potential errors through test design, method validation, or quality controls so that no harm comes to the patient. 

The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results.

Article Outline

1. Overview of Targeted NGS for Oncology Specimens
   1. General Considerations
   2. Targeted NGS Method Overview
      1. Sample Preparation
      2. Library Preparation
         1. Hybrid Capture NGS
         2. Amplification-Based NGS
      3. Sequencing
      4. Data Analysis
2. Considerations for Test Development, Optimization, and Familiarization
   1. Designing Panel Content
   2. Choosing Sequencing Platform and Sequencing Method
   3. Assessing Potential Sources of Error during the NGS Assay Development Process
   4. Optimization and Familiarization Process
      1. Preliminary Performance Specifications
      2. Library Complexity
      3. Establishing Criteria for Depth of Sequencing
3. NGS Test Validation
   1. Validation Protocol
   2. Types and Number of Samples Required for Test Validation
   3. PPA and PPV
   4. Repeatability/Reproducibility
   5. Reportable Range and Reference Range
   6. Limits of Detection
   7. Interfering Substances and Carryover
   8. Clinical Validation and Clinical Utility
   9. Validation of Bioinformatics Pipelines
   10. Validating a Modified Component of a Test or Platform
4. Implementation and Quality Control Metrics
   1. Specimen Requirements
   2. DNA Requirements
   3. Library Qualification and Quantification Requirements
   4. Core Metrics of Analytical Performance Quality Control
   5. Controls
   6. Confirmatory Testing
   7. Proficiency Testing
5. Validation Documentation and Summary
6. Summary
7. Disclaimer
8. Supplemental Data
9. References