Unknown

Dataset Information

0

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability.


ABSTRACT: Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Traditional experimental assays are laborious and time-consuming, and next-generation sequencing-based computational methods do not work on leukemia samples, paraffin-embedded samples, or patient-derived xenografts/organoids, due to the requirement of matched normal samples. Herein, we developed MSIsensor-pro, an open-source single sample MSI scoring method for research and clinical applications. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative site selection method to enable MSI detection without matched normal samples. We demonstrate that MSIsensor-pro is an ultrafast, accurate, and robust MSI calling method. Using samples with various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in both accuracy and computational cost. MSIsensor-pro is available at https://github.com/xjtu-omics/msisensor-pro and free for non-commercial use, while a commercial license is provided upon request.

SUBMITTER: Jia P 

PROVIDER: S-EPMC7393535 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

altmetric image

Publications

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability.

Jia Peng P   Yang Xiaofei X   Guo Li L   Liu Bowen B   Lin Jiadong J   Liang Hao H   Sun Jianyong J   Zhang Chengsheng C   Ye Kai K  

Genomics, proteomics & bioinformatics 20200201 1


Microsatellite instability (MSI) is a key biomarker for cancer therapy and prognosis. Traditional experimental assays are laborious and time-consuming, and next-generation sequencing-based computational methods do not work on leukemia samples, paraffin-embedded samples, or patient-derived xenografts/organoids, due to the requirement of matched normal samples. Herein, we developed MSIsensor-pro, an open-source single sample MSI scoring method for research and clinical applications. MSIsensor-pro  ...[more]

Similar Datasets

| S-EPMC3967115 | biostudies-literature
2024-04-08 | PXD046855 | Pride
| S-EPMC4529134 | biostudies-literature
| S-EPMC8424396 | biostudies-literature
| S-EPMC4723934 | biostudies-literature
| S-EPMC1906892 | biostudies-literature
| PRJNA1170349 | ENA
| PRJNA1170350 | ENA
| S-EPMC9714634 | biostudies-literature
| S-EPMC7146943 | biostudies-literature