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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Sanger Sequencing01:57

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Related Experiment Video

Updated: Sep 13, 2025

Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions
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An innovative full-size pathogenic tandem duplication mutation precise detection system based on next-generation

Li-Li Zhang1, Zhe Wang1, Ying Zhou1

  • 1Shanghai Tissuebank Biotechnology Co., Ltd., Shanghai, China.

Experimental Biology and Medicine (Maywood, N.J.)
|July 28, 2025
PubMed
Summary

A new system, ITDFinder, accurately detects internal tandem duplication (ITD) mutations in acute myeloid leukemia (AML) using next-generation sequencing. This tool improves ITD mutation assessment and patient prognosis, saving significant workload.

Keywords:
acute myeloid leukemiainternal tandem duplicationmutation detectionnext-generation sequencingprognosis

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Area of Science:

  • Genetics and Genomics
  • Hematology
  • Bioinformatics

Background:

  • Accurate identification of internal tandem duplication (ITD) mutations is crucial for acute myeloid leukemia (AML) diagnosis and prognosis.
  • Existing detection tools for ITD mutations are limited in scope and size range.
  • There is a need for a reliable and comprehensive system for ITD mutation assessment in AML.

Purpose of the Study:

  • To develop and validate a novel next-generation sequencing (NGS)-based system for accurate detection of ITD mutations in AML.
  • To establish a system capable of assessing ITD mutations across various size ranges.
  • To improve the clinical assessment and prognosis of AML patients through enhanced ITD mutation detection.

Main Methods:

  • Development of a short-read tandem duplication recognition system based on soft-clip analysis of NGS data.
  • Establishment of a lower detection limit comparable to capillary electrophoresis by adjusting reference values.
  • Validation of the system's concordance with capillary electrophoresis and its applicability to other tandem duplication mutations using simulated and clinical data.

Main Results:

  • An innovative NGS-based system, ITDFinder, was developed for accurate ITD mutation detection with a lower limit of 4% at 1000X sequencing depth.
  • ITDFinder demonstrated good consistency with capillary electrophoresis (mean difference: -0.0085) across various ITD lengths.
  • Clinical validation with 1,032 AML cases showed a 96.5% agreement rate between ITDFinder and capillary electrophoresis; simulation suggested applicability to BCOR-ITD and KMT2A-PTD mutations.

Conclusions:

  • The developed ITDFinder system accurately detects small-to large-sized ITDs and other pathogenic tandem duplication mutations.
  • This innovative system offers significant potential for accurate clinical assessment of ITD mutations, improving AML patient prognosis.
  • ITDFinder is expected to save 96.3% of the workload associated with ITD mutation detection.