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J Mol Diagn. 2019 Aug 22. pii: S1525-1578(19)30358-7. doi: 10.1016/j.jmoldx.2019.06.011. [Epub ahead of print]

A Novel Next-Generation Sequencing Approach to Detecting Microsatellite Instability and Pan-Tumor Characterization of 1000 Microsatellite Instability-High Cases in 67,000 Patient Samples.

Author information

1
Foundation Medicine, Inc., Cambridge, Massachusetts. Electronic address: strabucco@foundationmedicine.com.
2
Foundation Medicine, Inc., Cambridge, Massachusetts.
3
Department of Oncology Biomarker Development, Genentech, Inc., San Francisco, California.
4
Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
5
Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island.
6
Foundation Medicine, Inc., Cambridge, Massachusetts; Department of Pathology and Laboratory Medicine, UC Davis Health, Sacramento, California.

Abstract

Microsatellite instability (MSI) is an important biomarker for predicting response to immune checkpoint inhibitor therapy, as emphasized by the recent checkpoint inhibitor approval for MSI-high (MSI-H) solid tumors. Herein, we describe and validate a novel method for determining MSI status from a next-generation sequencing comprehensive genomic profiling assay using formalin-fixed, paraffin-embedded samples. This method is 97% (65/67) concordant with current standards, PCR and immunohistochemistry. We further apply this method to >67,000 patient tumor samples to identify genes and pathways that are enriched in MSI-stable or MSI-H tumor groups. Data show that although rare in tumors other than colorectal and endometrial carcinomas, MSI-H samples are present in many tumor types. Furthermore, the large sample set revealed that MSI-H tumors selectively share alterations in genes across multiple common pathways, including WNT, phosphatidylinositol 3-kinase, and NOTCH. Last, MSI is sufficient, but not necessary, for a tumor to have elevated tumor mutation burden. Therefore, MSI can be determined from comprehensive genomic profiling with high accuracy, allowing for efficient MSI-H detection across all tumor types, especially those in which routine use of immunohistochemistry or PCR-based assays would be impractical because of a rare incidence of MSI. MSI-H tumors are enriched in alterations in specific signaling pathways, providing a rationale for investigating directed immune checkpoint inhibitor therapies in combination with pathway-targeted therapies.

PMID:
31445211
DOI:
10.1016/j.jmoldx.2019.06.011
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