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Summary

Next-generation sequencing (NGS) assays demonstrate high interlaboratory analytical performance for inherited disorders. Laboratories consistently achieved excellent sensitivity and specificity in variant detection from 2016-2020.

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Area of Science:

  • Genetics and Genomics
  • Molecular Diagnostics
  • Laboratory Medicine

Background:

  • Next-generation sequencing (NGS) is crucial for diagnosing inherited disorders.
  • Limited data exist on the interlaboratory analytical performance of these diagnostic assays.
  • The College of American Pathologists (CAP) initiated the NGS Germline Program to address this gap.

Purpose of the Study:

  • To report on the interlaboratory analytical performance of NGS-based germline testing.
  • To analyze the evolution of laboratory testing practices within the CAP NGS Germline Program from 2016-2020.
  • To evaluate the consistency and accuracy of variant detection across participating laboratories.

Main Methods:

  • Analysis of results from the CAP NGS Germline Program (2016-2020).
  • Evaluation of self-reported laboratory testing practices, including test offerings (panels, exomes, genomes).
  • Assessment of interlaboratory analytical performance metrics such as sensitivity and specificity for variant detection.

Main Results:

  • 297 laboratories participated between 2016-2020, with evolving test offerings.
  • Median detection percentage for variants ranged from 94.3% to 100%, with 100% accuracy for reference positions.
  • Laboratories consistently met detection thresholds (≥90% variant detection) and specificity thresholds (≥95%).

Conclusions:

  • Laboratories participating in the CAP NGS Germline Program have shown consistently high analytical performance since its inception.
  • The median sensitivity and specificity for detecting sequence variants (SNVs, indels) were 100.0%.
  • These findings support the reliability of NGS-based assays for diagnosing inherited disorders.