AMP Issues Consensus Guidelines for NGS Bioinformatics Pipelines

The Association for Molecular Pathology (AMP) published 17 consensus recommendations for the validation of clinical next-generation sequencing bioinformatics pipelines. The report, "Standards and Guidelines for Validating Next Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists," is published in the January 2018 issue of the Journal of Molecular Diagnostics.

AMP convened a multidisciplinary expert working group, including representatives of the College of American Pathologists and the American Medical Informatics Association to summarize current knowledge, expose challenges, and provide guidance on how to develop, implement, and validate high-quality, bioinformatics pipelines. The report emphasizes the critical role of the properly trained molecular laboratory professional and recommends practical advice for the development of bioinformatics pipelines. Some of the recommendations include:

• Clinical laboratories offering NGS testing should perform bioinformatics pipeline validation, but only after completion of design, development, and optimization of the bioinformatics pipeline and all of its components.

• Supplemental validation is required whenever a significant change is made to any component of the bioinformatics pipeline.

• A qualified medical professional with appropriate training in NGS interpretation should oversee the validation process.

• The pipeline should ensure the security of identifiable patient information.

• The identity of the sample should be preserved throughout each step of the NGS bioinformatics pipeline, with a minimum of four unique identifiers.

• The bioinformatics pipeline is part of the test procedure, and its components and processes must be documented according to laboratory accreditation standards and regulations.

• Validation of the bioinformatics pipeline should include confirmation of a representative set of variants with high-quality independent data.

• Methods used to alter or filter sequence reads at any point in the pipeline should be validated to ensure that the data presented for interpretation accurately and reproducibly represents the sequence in the specimen. All methods should be fully documented.