Recommendations for in silico approaches for validating next-generation molecular sequencing analysis pipelines
The Association for Molecular Pathology (AMP), a global, molecular diagnostic professional society, today published consensus recommendations for the use of in silico approaches for validating Next-Generation Sequencing (NGS) data analysis pipelines.
The manuscript, “Recommendations for the Use of In Silico Approaches for Next Generation Sequencing Bioinformatic Pipeline Validation: A Joint Report of the Association for Molecular Pathology, Association for Pathology Informatics, and College of American Pathologists,” was released online ahead of publication in The Journal of Molecular Diagnostics.
“As more laboratories around the country use in silico data to simulate variants to help validate the performance of clinical NGS data analysis pipelines, clinical laboratory professionals may need an aid for understanding both the value these methods bring and the important nuances and limitations of these approaches,” said Justin Zook, Ph.D., Co-Chair of the AMP In Silico Pipeline Validation Working Group and Co-Leader of the Biomarker and Genomic Sciences Group at the National Institute of Standards and Technology.
“AMP convened a panel of subject matter experts from AMP, Association for Pathology Informatics, and College of American Pathologists to explore the advantages and disadvantages of these various types of in silico data. This new JMD report summarizes our key findings and provides useful recommendations to help clinical laboratory professionals select the most appropriate format for their specific purpose.”
AMP devotes significant resources to developing evidence-based and consensus-driven practice guidelines to help establish essential elements of high-quality test design, such as analytical and clinical validity. The In Silico Pipeline Validation Working Group led the collective effort to review the available published literature and analyze the different types of in silico data and how they can be used in the clinical molecular diagnostic laboratory.
The new report also presents survey data on current use cases and highlights potential future applications. The team offered the following expert consensus opinion general recommendations based on these findings.
Consensus Recommendations
“AMP is committed to collaborating with the broader clinical laboratory community to help identify areas of opportunity to continuously improve clinical practice, molecular diagnostic testing, and patient care,” said Eric J. Duncavage, MD, Co-Chair of the AMP In Silico Pipeline Validation Working Group and Professor of Pathology and Immunology at the Washington University School of Medicine in St. Louis.
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