Implementation, Evolution, and Laboratory Performance of Methods-Based Proficiency Testing for Next-Generation...

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.