AMP offers recommendations for in silico approaches for validating next-generation sequencing analysis pipelines

Nov. 4, 2022
Latest joint consensus guideline authored by representatives from AMP, Association for Pathology Informatics, and College of American Pathologists.

The Association for Molecular Pathology (AMP), the premier global, molecular diagnostic professional society, 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.  

Consensus Recommendations: 

1. The laboratory may use in silico data files to supplement NGS analytical validation, particularly to assess analytical sensitivity or false negative rates for specific variants; however, in silico data files cannot supplant the use of physical samples (e.g., patient samples).  

2. The laboratory should understand the functional limitations of the type(s) of in silico data being utilized.  

3. The laboratory should understand the limitations of most in silico data for assessing performance in particular genome contexts and variant types susceptible to systematic sequencing and mapping errors.

4. The laboratory may consider using in silico samples for minor updates to clinical bioinformatics software pipelines.  

5. Commercial vendors and internal pipeline developers should include options in their analysis pipelines to facilitate easier in silico data file import and analysis by clinical laboratories. 

AMP release