A novel algorithm for the detection of microsatellite instability in endometrial cancer using next‑generation sequencing data

Zhou,Bing; Wang,Yu; Ding,Lu; Tian,Xiaolei; Sun,Wu; Zhang,Wei; Liu,Yin-Hua

doi:10.3892/ol.2024.14832

A novel algorithm for the detection of microsatellite instability in endometrial cancer using next‑generation sequencing data

Authors:
- Bing Zhou
- Yu Wang
- Lu Ding
- Xiaolei Tian
- Wu Sun
- Wei Zhang
- Yin-Hua Liu
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Affiliations: Department of Pathology, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China, Department of Gynecology, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
Published online on: December 3, 2024 https://doi.org/10.3892/ol.2024.14832
Article Number: 86
Copyright: © Zhou et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The molecular‑based detection of microsatellite instability (MSI) in endometrial cancer is complex, due to the low sensitivity of PCR and a lack of standardization in next‑generation sequencing (NGS) methods. In the present study, sequenced data were obtained from an NGS panel following the addition of five commonly used microsatellite loci. Subsequently, a novel algorithm, namely MSIPeak, was developed for data analysis. Results of the present study demonstrated that MSI data obtained using MSIPeak were presented in a peak, using a threshold of 1.10 to distinguish stable and unstable loci. MSIPeak was further validated using synthetic DNA samples and endometrial cancer tissue and the results were compared with the immunohistochemical analysis‑determined mismatch repair status. The PCR results demonstrated a 3‑base‑pair (bp) deletion in synthetic DNA samples, compared with 1‑ and 2‑bp deletion controls. Results obtained using MSIPeak demonstrated notable differences in peak profiles and positive scores in synthetic DNA samples with 1‑, 2‑ and 3‑bp deletions, compared with controls. Thus, the results of the present study demonstrated that NGS‑based MSI detection exhibited a higher sensitivity compared with PCR. In addition, NGS‑based MSI detection exhibited higher levels of repeatability and applicability compared with other MSI‑NGS‑based methods, such as MSISensor2 and MANTIS. Collectively, the results of the present study highlighted that the combination of MSIPeak and NGS exhibits potential in the detection of cancer.

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