J Lab Med Qual Assur.  2020 Mar;42(1):48-53. 10.15263/jlmqa.2020.42.1.48.

Three-Year Experience of an External ProficiencyTesting Survey for Next-Generation Sequencing-Based Testing for Germline Mutation

Affiliations
  • 1Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Korea
  • 2Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea

Abstract

Background
Next-generation sequencing is a powerful technology thatallows simultaneous analysis of several genes but also demands a welldesignedquality management system owing to its complexity. We aimed toanalyze the results of next-generation sequencing (NGS)-germline proficiencytesting (PT) survey performed by the Korean Association of External QualityAssessment Service during 2017–2019 to assess the current status of theNGS-based genetic testing in Korea.
Methods
The recent 3-year results from the PT survey were investigated.During this period, PT survey was performed twice every year with two orthree challenges per round. Correct results (%) were calculated from alltested regions; the trend by year and variation type was analyzed and theprobable causes estimated.
Results
During this period, the number of participating laboratoriesincreased from 5 to 22. The correct results were 97.2% in average andshowed a gradual increase with year. The most common ‘unacceptable’results were false-negative or false-positive, followed by inappropriatenomenclature and zygosity assignment.
Conclusions
The PT survey shows that the overall performance of NGSlaboratories in Korea is highly confident, although some improvements maybe needed. A method-based PT survey for the NGS test serves as a usefulapproach to assess the performance of NGS laboratories.

Keyword

Next-generation sequencing; Proficiency test; Method-based proficiency test
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