학술논문
ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application
Document Type
Report
Author
Source
BMC Bioinformatics. February 23, 2023, Vol. 24 Issue 1
Subject
Language
English
ISSN
1471-2105
Abstract
Author(s): Sungyoung Lee[sup.1,2] , Choong-Hyun Sun[sup.3] , Heejun Jang[sup.4] , Daeyoon Kim[sup.4] , Sung-Soo Yoon[sup.4,5] , Youngil Koh[sup.4,5] , Seung Chan Na[sup.6] , Sung Im Cho[sup.6] , Man Jin Kim[sup.1] [...]
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository. Keywords: Internal tandem duplication, Next-generation sequencing, Acute myeloid leukemia, fragment analysis
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository. Keywords: Internal tandem duplication, Next-generation sequencing, Acute myeloid leukemia, fragment analysis