Microsatellite instability in prostate cancer by PCR or next-generation sequencing

Jennifer A Hempelmann,Colin C Pritchard,Michael T Schweizer,Bruce Montgomery,Tamara L Lotan,Eric Q Konnick,Christina M Lockwood,Stephen J Salipante,Peter S Nelson,Nola Klemfuss,Emmanuel S Antonarakis

doi:10.1186/s40425-018-0341-y

Abstract

BackgroundMicrosatellite instability (MSI) is now being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer. Yet current molecular diagnostic tests for MSI have not been evaluated for use in prostate cancer.MethodsWe evaluated two next-generation sequencing (NGS) MSI-detection methods, MSIplus (18 markers) and MSI by Large Panel NGS (> 60 markers), and compared the performance of each NGS method to the most widely used 5-marker MSI-PCR detection system. All methods were evaluated by comparison to targeted whole gene sequencing of DNA mismatch-repair genes, and immunohistochemistry for mismatch repair genes, where available.ResultsIn a set of 91 prostate tumors with known mismatch repair status (29-deficient and 62-intact mismatch-repair) MSIplus had a sensitivity of 96.6% (28/29) and a specificity of 100% (62/62), MSI by Large Panel NGS had a sensitivity of 93.1% (27/29) and a specificity of 98.4% (61/62), and MSI-PCR had a sensitivity of 72.4% (21/29) and a specificity of 100% (62/62).ConclusionsWe found that the widely used 5-marker MSI-PCR panel has inferior sensitivity when applied to prostate cancer and that NGS testing with an expanded panel of markers performs well. In addition, NGS methods offer advantages over MSI-PCR, including no requirement for matched non-tumor tissue and an automated analysis pipeline with quantitative interpretation of MSI-status.

Highlights

Microsatellite instability (MSI) is being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer
There is an immediate need for a highly sensitive and specific diagnostic assay for MSI targeted to specific tumor types. To address this need in prostate cancer, we evaluated two next-generation sequencing (NGS) MSI-detection methods, MSIplus [22] and MSI by Large Panel NGS [23], for efficacy in prostate cancer and compared the performance characteristics of each method to the MSI-PCR based on the 5-marker Bethesda panel [18] (Promega, Madison, WI, USA). We compared both NGS methods and MSI-PCR to targeted deep sequencing of MMR genes: because DNA mismatch repair (dMMR) is caused by bi-allelic gene mutation rather than epigenetic silencing in prostate cancer [11], deep sequencing can provide a definitive “gold-standard” diagnosis
Establishing a validation sample set We selected validation samples from 4 prostate cancer series compromising primary and metastatic disease. dMMR is caused by bi-allelic gene mutation rather than epigenetic silencing in prostate cancer [11]

Summary

Introduction

Microsatellite instability (MSI) is being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer. Microsatellite instability (MSI) is characterized by mutations in repetitive DNA sequence tracts, caused by a failure of the DNA mismatch repair system to correct these errors. In May of 2017, the U.S Food and Drug Administration (FDA) granted accelerated approval of an immunotherapy-based anti-PD-1 cancer treatment (pembrolizumab) for patients whose cancers have MSI or dMMR [1]. This is the first time the FDA has approved a drug based on the genetic characteristics of a tumor alone, regardless of the tumor’s original location (“tumor agnostic”). MSI and dMMR have been reported in a subset of tumors ranging from ~ 1% in primary to up to 12% of metastatic cancers [10,11,12,13]

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Discussion

Conclusion