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

(E-pub Ahead of Print)

Author(s): Binsheng He, Jialiang Yang, Geng Tian, Pingping Bing, Jidong Lang*.

Journal Name: Current Bioinformatics

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Abstract:

Thymidylate synthase (TS) is an important target for folicacid 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 TYMS gene encoding TS is critical in clinical applications. With the development of the 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. In this study, we have developed a novel method based on "paired seed sequence distance” (PSSD) to detect the variable number of tandem repeat (VNTR) mutation for TYMS. 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, next-generation sequencing (NGS), TYMS, paired seed sequence distance, the variable number of tandem repeat (VNTR), similar polymorphism analyses

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Article Details

(E-pub Ahead of Print)
DOI: 10.2174/1574893615999200505074805
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