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Background Currently,  FLT3  internal tandem duplication (ITD) is tested by fragment analysis. With next-generation sequencing (NGS), however, not only  FLT3  ITD but also other mutations can be detected, which can provide more genetic information on disease. Methods We retrospectively reviewed the results of two tests—fragment analysis and a custom-designed, hybridization capture-based, targeted NGS panel—performed simultaneously. We used the Pindel algorithm to detect  FLT3  ITD mutations. Results Among 277 bone marrow aspirate samples tested by NGS and fragment analysis, the results revealed 99.6% concordance in  FLT3  ITD detection. Overall, the allele frequency (AF) attained by NGS positively correlated with the standard allelic ratio (AR) attained by fragment analysis, with a Spearman correlation coefficient (r) of 0.757 (95% confidence interval: 0.627–0.846;  p  &lt; 0.001). It was concluded that an AF of 0.11 attained by NGS is the most appropriate cutoff value (with 85.3% sensitivity and 86.7% specificity) for high mutation burden criterion presented by guidelines. Conclusion Sensitive  FLT3  ITD detection with comprehensive information of other mutation offered by NGS could be a useful tool in clinical laboratories. Future studies will be needed to evaluate and standardize NGS AF cutoff to predict actual clinical outcomes.

diagnostic pathology

A comparative study of next-generation sequencing and fragment analysis for the detection and allelic ratio determination of FLT3 internal tandem duplication