A novel NGS-based microsatellite instability (MSI) status classifier with 9 loci for colorectal cancer patients

Kai Zheng,Nan Fang,Xichuan Li,Chunze Zhang,Rong Du,Jie Zhang,Dongdong Li,Ningning Chai,Jingbo Zhang,Hua Wan,Lina Liu,Qixi Wu,Guangyu Shan

doi:10.1186/s12967-020-02373-1

Abstract

BackgroundWith the recent emergence of immune checkpoint inhibitors, microsatellite instability (MSI) status has become an important biomarker for immune checkpoint blockade therapy. There are growing technical demands for the integration of different genomic alterations profiling including MSI analysis in a single assay for full use of the limited tissues.MethodsTumor and paired control samples from 64 patients with primary colorectal cancer were enrolled in this study, including 14 MSI-high (MSI-H) cases and 50 microsatellite stable (MSS) cases determined by MSI-PCR. All the samples were sequenced by a customized NGS panel covering 2.2 MB. A training dataset of 28 samples was used for selection of microsatellite loci and a novel NGS-based MSI status classifier, USCI-msi, was developed. NGS-based MSI status, single nucleotide variant (SNV) and tumor mutation burden (TMB) were detected for all patients. Most of the patients were also independently detected by immunohistochemistry (IHC) staining.ResultsA 9-loci model for detecting microsatellite instability was able to correctly predict MSI status with 100% sensitivity and specificity compared with MSI-PCR, and 84.3% overall concordance with IHC staining. Mutations in cancer driver genes (APC, TP53, and KRAS) were dispersed in MSI-H and MSS cases, while BRAF p.V600E and frameshifts in TCF7L2 gene occurred only in MSI-H cases. Mismatch repair (MMR)-related genes are highly mutated in MSI-H samples.ConclusionWe established a new NGS-based MSI classifier, USCI-msi, with as few as 9 microsatellite loci for detecting MSI status in CRC cases. This approach possesses 100% sensitivity and specificity, and performed robustly in samples with low tumor purity.

Highlights

With the recent emergence of immune checkpoint inhibitors, microsatellite instability (MSI) status has become an important biomarker for immune checkpoint blockade therapy
Germline mutations in mismatch repair (MMR) proteins are associated with the pathogenesis of Lynch syndrome, which accounts for approximately 20% MMR-deficient colorectal cancer (CRC) [4]
We developed a novel Microsatellite instability (MSI) classifier named USCI-msi based on Next-Generation Sequencing (NGS) data with 9 microsatellite loci

Summary

Introduction

With the recent emergence of immune checkpoint inhibitors, microsatellite instability (MSI) status has become an important biomarker for immune checkpoint blockade therapy. There are growing technical demands for the integration of different genomic alterations profiling including MSI analysis in a single assay for full use of the limited tissues. Microsatellite instability (MSI) represents the nucleotide insertions or deletions in the microsatellite loci. The DNA mismatch repair (MMR) proteins, e.g. MLH1, Zheng et al J Transl Med (2020) 18:215. The germline or somatic inactivation of MMR genes could in turn result in MSI. Germline mutations in MMR proteins are associated with the pathogenesis of Lynch syndrome, which accounts for approximately 20% MMR-deficient (dMMR) colorectal cancer (CRC) [4]. For sporadic CRC, somatic mutations in microsatellite loci were found in 10% to 15% of cases [5]

Methods

Results

Discussion

Conclusion