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Published on: July 22, 2020
A novel NGS-based microsatellite instability (MSI) status classifier with 9 loci for colorectal cancer patients
Kai Zheng1, Hua Wan2, Jie Zhang3
1Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 300121, China.
Background:
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.
Methods:
Tumor 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.
Results:
A 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.
Conclusion:
We 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.
Insights
A new next-generation sequencing (NGS) classifier, USCI-msi, accurately determines microsatellite instability (MSI) status in colorectal cancer (CRC) using only 9 loci. This method is highly sensitive and specific, aiding biomarker selection for immunotherapy.
Area of Science:
- Oncology
- Genomics
- Biomarker Discovery
Background:
- Microsatellite instability (MSI) is a key biomarker for immune checkpoint inhibitor therapy.
- Limited tissue samples necessitate integrated genomic profiling assays, including MSI analysis.
Purpose of the Study:
- To develop and validate a novel next-generation sequencing (NGS)-based classifier for microsatellite instability (MSI) status in colorectal cancer (CRC).
- To assess the performance of the NGS classifier in conjunction with other genomic alterations like tumor mutation burden (TMB).
Main Methods:
- Developed a 9-loci NGS-based MSI classifier (USCI-msi) using a training dataset of 28 colorectal cancer samples.
- Sequenced 64 primary CRC tumor samples with a customized 2.2 MB NGS panel.
- Validated MSI status, single nucleotide variants (SNV), and TMB using NGS and immunohistochemistry (IHC).
Main Results:
- The USCI-msi classifier achieved 100% sensitivity and specificity for MSI detection compared to MSI-PCR.
- Achieved 84.3% overall concordance with IHC staining for MSI status.
- Identified specific gene mutations (BRAF p.V600E, TCF7L2) exclusive to MSI-high cases and high mutation rates in MMR-related genes.
Conclusions:
- Established USCI-msi, a robust NGS-based MSI classifier for CRC, utilizing minimal microsatellite loci.
- Demonstrated high accuracy and reliability of the NGS approach, even in samples with low tumor purity.
- The classifier supports integrated genomic profiling for improved biomarker assessment in CRC.
