Ann Lab Med.  2019 Nov;39(6):515-523. 10.3343/alm.2019.39.6.515.

Korean Society for Genetic Diagnostics Guidelines for Validation of Next-Generation Sequencing-Based Somatic Variant Detection in Hematologic Malignancies

  • 1Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
  • 2Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Korea.
  • 3Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.


Next-generation sequencing (NGS) is currently used in the clinical setting for targeted therapies and diagnosis of hematologic malignancies. Accurate detection of somatic variants is challenging because of tumor purity, heterogeneity, and the complexity of genetic alterations, with various issues ranging from high detection design to test implementation. This article presents guidelines developed through consensus among a panel of experts from the Korean Society for Genetic Diagnostics. They are based on experiences with the validation processes of NGS-based somatic panels for hematologic malignancies, with reference to previous international recommendations. These guidelines describe basic parameters with emphasis on the design of a validation protocol for NGS-based somatic panels to be used in practice. In addition, they suggest thresholds of key metrics, including minimum coverage, mean coverage with uniformity index, and minimum variant allele frequency, for the initial diagnosis of hematologic malignancies.


Next-generation sequencing; Validation; Somatic variant; Guidelines; Panels; Hematologic malignancies

MeSH Terms

Gene Frequency
Hematologic Neoplasms*
Population Characteristics


  • Fig. 1 Overview of validation process for somatic variants in hematologic malignancies using NGS testing.*Samples include patient samples, validated cell lines, and/or commercial controls.Abbreviations: NGS, next-generation sequencing; LoD, limit of detection; PPA, positive percentage agreement; PPV, positive predictive value; AF, allele frequency.

  • Fig. 2 An example of Step 1 validation (pilot test).*Pooled samples can comprise one short deletion, one short insertion, and one long insertion in different regions of the patient samples.Abbreviations: AF, allele frequency; RM, reference material; SNV, single-nucleotide variant; indel, insertion and/or deletion.

  • Fig. 3 An example of Step 2 validation (formal validation) with 64 samples (including separately bar-coded samples from the same patient/RMs/commercial positive controls). For LoD validation, samples with various VAF were guaranteed by dilution with RM.*Pooled samples can be comprised of one short deletion, one short insertion, and one long insertion in different regions of the patient samples.Abbreviations: indels, insertions and/or deletions; RM, reference material; VAF, variant allele frequency; SNV, single nucleotide variant; LoD, limit of detection.

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