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Detecting TYMS Tandem Repeat Polymorphism by the PSSD Method Based on Next-Generation Sequencing

[ Vol. 15 , Issue. 10 ]

Author(s):

Binsheng He*, Jialiang Yang, Geng Tian, Pingping Bing* and Jidong Lang*   Pages 1153 - 1159 ( 7 )

Abstract:


Background: Thymidylate Synthase (TS) is an important target for folic acid inhibitors such as pemetrexed, which has considerable effects on the first-line treatment, second-line treatment and maintenance therapy for patients with late-stage Non-Small Cell Lung Cancer (NSCLC). Therefore, detecting mutations in the TYMS gene encoding TS is critical in clinical applications. With the development of Next-Generation Sequencing (NGS) technology, the accuracy of TYMS mutation detection is getting higher and higher. However, traditional methods suffer from false positives and false-negatives caused by factors like limited sequencing read length and sequencing errors.

Objective: A method was needed to overcome the short sequencing read length and sequencing errors of NGS to make the detection of TYMS more accurate.

Methods: In this study, we developed a novel method based on "Paired Seed Sequence Distanceā€ (PSSD) to detect the Variable Number of Tandem Repeat (VNTR) mutation for TYMS.

Results: With the 121 samples validated by sanger, the consistency rate of PSSD method was 85.95% (104/121), higher than the strict matching method (78.51% (95/121)). The consistency rate of the two methods was 89.26% (108/121). We also found that the PSSD method was significantly better than the strict matching method, especially in the 4R typing.

Conclusion: Our method not only improves the detection rate and accuracy of TYMS VNTR mutations but also avoids problems caused by sequencing errors and limited sequencing length. This method provides a new solution for similar polymorphism analyses and other sequencing analyses.

Keywords:

Thymidylate synthase (TS), next generation sequencing (NGS), Paired seed sequence distance (PSSD), tandem repeat, polymorphism typing, cancer.

Affiliation:

Academician Workstation, Changsha Medical University, Changsha 410219, Academician Workstation, Changsha Medical University, Changsha 410219, Geneis (Beijing) Co. Ltd., Beijing, 100102, Academician Workstation, Changsha Medical University, Changsha 410219, Geneis (Beijing) Co. Ltd., Beijing, 100102



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