Abstract 2080: Tumor microsatellite instability detection method using paired tumor-normal sequence data
Authors: Yuan Hongling , Wang Danhua , Zhu Honglin 
Published: July 2021

Background: Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases. MMR gene mutations usually lead to the loss of MMR proteins, resulting in high instability of tumor DNA microsatellites (MSI-H), and leading to a high tumor mutation burden (TMB-H). In current clinical practice, MSI detection is performed by experimental methods such as MSI-PCR and MMR-IHC. However, the PCR-based detection procedure is laborious and time-consuming, the accuracy of the results depends on the naked eye judgment of the analysts. With the development of next-generation sequencing (NGS) technology, a large number of MSI detection software based on high-throughput sequencing data have been developed. In this study, we compared the two methods provide a computational method that quantifies MSI status based on genome sequencing data.

Methods: 2523 tested samples, including 80 MSI-H samples and 2443 MSS samples, detected by MSI-PCR and NGS-Seq simultaneously, were enrolled in this study. In the MSI-PCR method, MSI status was classified as Microsatellite stable (MSS) and MSI-high (MSI-H, over 2 markers unstable). For the NGS-Seq method, the status of 54 microsatellite site was evaluated by the MSI sensor (https://github.com/ding-lab/msisensor) and the proportion of unstable microsatellite site (RatioUMS) was calculated, and MSI status was classified as MSS (RatioUMS&lt;35), MSS-To Be Determined (MSI-TBD, 35≤RatioUMS≤55), and MSI-H (RatioUMS&gt;55). For MSI-TBD, either TMB is greater than 30 (TMB&gt;30) or TMB is greater than 10 and had a non-silent mutation in an MMR gene (TMB&gt;10&MMR+), MSI-H is considered, otherwise, MSS is considered.

Results: In our test, NGS results were inconsistent with MSI-PCR method in 8 samples, among which 5 samples were categorized incorrectly by MSI-PCR after reverification. According to the above results, the consistency of two methods was 99.9%. We also tested the classifier using 114 microsatellite sites in 425 samples and 309 microsatellite sites in 2098 samples. Compared with MSI-PCR, the consistency was 100% and 99.6%, respectively. For the 25 MSI-TBD samples, adding two parameters, MMR gene mutation and TMB, greatly improved the accuracy of the judgment.

Conclusion: The results show NGS method are highly consistent with the gold standard MSI-PCR, and the judgmental errors caused in MSI-PCR by human factors can be avoided. The different number of microsatellite sites used in the NGS method has little effect on the final results. NGS approach offers the advantages to simultaneous detection of predictive markers, including MSI, TMB and clinically relevant genomic alterations, will save valuable material, time and costs, which can provide more comprehensive and reasonable recommendations for medication and treatment.

Citation Format: Hongling Yuan, Danhua Wang, Honglin Zhu. Tumor microsatellite instability detection method using paired tumor-normal sequence data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2080.