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

J Mol Diagn. 2018 Jan;20(1):4-27. doi: 10.1016/j.jmoldx.2017.11.003. Epub 2017 Nov 21.


Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care. To address this unmet need, the Association of Molecular Pathology, with organizational representation from the College of American Pathologists and the American Medical Informatics Association, has developed a set of 17 best practice consensus recommendations for the validation of clinical NGS bioinformatics pipelines. Recommendations include practical guidance for laboratories regarding NGS bioinformatics pipeline design, development, and operation, with additional emphasis on the role of a properly trained and qualified molecular professional to achieve optimal NGS testing quality.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / standards*
  • Guidelines as Topic*
  • High-Throughput Nucleotide Sequencing / standards*
  • Humans
  • Laboratories
  • Pathology, Molecular / standards*
  • Reproducibility of Results
  • United States