Innovation: AMP Issues New Guidelines for NGS Pipeline Validation

Molecular next-generation sequencing (NGS) tests have spurred tremendous growth in the lab industry. But as often happens with innovation, NGS technology may be moving faster than development of clinical protocols. Accordingly, the newly published guidelines from the Association for Molecular Pathology (AMP) for validation of clinical bioinformatics pipelines are of special significance. Key AMP recommendations for clinical labs developing NGS testing include:

• Performance of bioinformatics pipeline validation but only after completion of design, development and optimization of the bioinformatics pipeline and all its components;
• Supplemental validation after a significant change is made to any pipeline component;
• Oversight of the validation process by a qualified medical professional with appropriate training in NGS interpretation;
• Ensuring the confidentiality and security of identifiable patient information in the pipeline;
• Preserving sample identity with a minimum of four unique identifiers throughout each step of the pipeline;
• Being cognizant of the fact that the bioinformatics pipeline is part of the test procedure, and its components and processes must be documented according to laboratory accreditation standards and regulations;
• Including confirmation of a representative set of variants with high-quality independent data as part of validation;
• Validating methods used to alter or filter sequence reads at any point in the pipeline to ensure that the data presented for interpretation accurately and reproducibly represents the sequence in the specimen; and
• Fully documenting all pipeline methods.