The sensitivity of the FLT3-ITD detection method is an important consideration when diagnosing acute myeloid leukemia

Sakaguchi, Masahiro; Nakajima, N.; Yamaguchi, Hiroki; Najima, Yuho; Shono, Katsuhiro; Marumo, Atsushi; Omori, Ikuko; Fujiwara, Y.; Terada, Kazuki; Yui, Shunsuke; Wakita, Satoshi; Mitaya, Miho; Arai, Kohei; Kitano, Tomoaki; Doki, Noriko; Inokuchi, Koiti

doi:10.1016/j.lrr.2020.100198

Cited by 11 publications

(17 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The AR was evaluated by dividing the area under the curve of the mutated fragment’s peak by that of the wild-type fragment’s peak. Although robust, this technique has several limitations: (i) the lower limit of quantification of the AR is high, generally at least 1% [ 14 , 15 ], (ii) the determination of the size of the ITD using the scale is approximate, (iii) the exact position of insertion and complete sequence of the ITD are not available [ 16 , 17 ] and (iv) sample multiplexing cannot be performed (v) quantification of very large insertions might be biased. Development of high-throughput sequencing enabled the detection of several genetic alterations in a single sequencing run and has the potential to overcome several of those limitations.…”

Section: Introductionmentioning

confidence: 99%

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

et al. 2022

View full text Add to dashboard Cite

Background Internal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3-ITDs in HTS data. Results Our algorithm (FiLT3r) focuses on the k-mers from reads covering FLT3 exons 14 and 15. We show that those k-mers bring enough information to accurately detect, determine the length and quantify FLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software. Conclusion FiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r. The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.

show abstract

Section: Introductionmentioning

confidence: 99%

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

et al. 2022

View full text Add to dashboard Cite

show abstract

“…FLT3 ITD mutation is a well-known predictive factor for poor prognosis in AML [ 12 ]. According to recommendations, the higher relapse rates and shorter overall survival times associated with FLT3 ITDs are influenced by mutation burden, at the boundary of 0.5, such that a highly accurate measurement of AR is necessary [ 13 ]. Patients with FLT3 ITD mutations carry a particularly poor prognosis such that allogeneic bone marrow transplantations during the first period of remission in this population are usually performed [ 14 , 15 ].…”

Section: Discussionmentioning

confidence: 99%

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

Kim

Lee

et al. 2022

Diagn Pathol

View full text Add to dashboard Cite

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 < 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.

show abstract

“…FLT3 was analyzed for internal tandem duplication (ITD) by PCR amplification followed by gel electrophoresis, for which the sensitivity of detection is recognized as being about 5% FLT3-ITD variant allele frequency (VAF) [6]. The patient was diagnosed as having AML with mutated NPM1 according to the WHO classification.…”

Section: Case Reportmentioning

confidence: 99%

Myelomonocytic differentiation of leukemic blasts accompanied by differentiation syndrome in a case of FLT3-ITD-positive AML treated with gilteritinib

Kondo¹,

Onozawa

Fujisawa

et al. 2021

Hematology

View full text Add to dashboard Cite

Fms-like tyrosine kinase 3 (FLT3) is one of the most frequently mutated genes in acute myelogenous leukemia (AML) and the mutation is associated with poor prognosis of patients. Two distinct types of activating mutations have been identified in AML samples. One is internal tandem duplications in the juxtamembrane domain (FLT3-ITD) and the other is point mutations in the tyrosine kinase domain (FLT3-TKD). Gilteritinib is a FLT3 inhibitor that inhibits both FLT3-ITD and FLT3-TKD. It was reported that differentiation of leukemic blasts accompanied by differentiation syndrome occurs in some patients treated with gilteritinib. However, information about the precise clinical course is limited, and appropriate management of differentiation syndrome has not been established. We report a case of relapsed AML with FLT3-ITD that was treated with gilteritinib. Analysis of the FLT3-ITD variant allele frequency (VAF) revealed that FLT3-ITD VAF was not decreased despite achievement of complete remission with incomplete hematologic recovery. Remarkable increases of monocytes and granulocytes accompanied by differentiation syndrome were observed at 6 months after the initiation of gilteritinib treatment. Intermittent chemotherapy with low-dose cytarabine and mitoxantrone was effective for reducing myelomonocytosis and resolving differentiation syndrome.

show abstract

The sensitivity of the FLT3-ITD detection method is an important consideration when diagnosing acute myeloid leukemia

Cited by 11 publications

References 16 publications

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

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

Myelomonocytic differentiation of leukemic blasts accompanied by differentiation syndrome in a case of FLT3-ITD-positive AML treated with gilteritinib

Contact Info

Product

Resources

About