Report of the Korean Association for External Quality Assessment of Next-Generation Sequencing Analysis for Somatic Variants in Hematologic Malignancies (2021–2025)

Next-generation sequencing (NGS) is increasingly being used to guide diagnosis, risk stratification, and treatment decisions in hematologic malignancies.Ensuring inter-laboratory concordance through external quality assessment (EQA) is thus essential.The association evaluated a nationwide NGS EQA program for somatic variants in hematologic malignancies conducted in Korea from 2021 to 2025.Each round included one BAM file and one DNA sample, each with 24 predefined target regions.Participating laboratories reported Tier I/II variants with a variant allele frequency (VAF) 10% using Human Genome Variation Society (HGVS) nomenclature.Acceptance rates were calculated for each reported variant, and the characteristics and causes of unacceptable results were reviewed.Participating laboratories increased from 19 to 29 over 10 rounds.Among 35 included Tier I/II variants, 19 achieved 100% acceptance and 15 showed 80% acceptance.The lowest acceptance rate (65.4%) was observed for an IKZF1 nonsense variant.Of 40 unacceptable responses associated with 13 of 20 specimens, 24 were false negatives, 7 were false positives, and 9 were due to non-standard or incorrect HGVS nomenclature.False results were frequently associated with homopolymer or repeat regions and with ASXL1 and NPM1 insertion/deletion variants.The Korean national EQA program demonstrated high overall concordance for NGS-based somatic variant testing in hematologic malignancies, while illuminating specific challenges related to difficult sequence contexts, low-VAF variants, and standardized variant nomenclature.Continuous EQA participation, adherence to international reporting recommendations, and targeted education will be crucial to further improve clinical NGS reporting accuracy and standardization.