Study demonstrates Next-Generation Sequencing can determine microsatellite instability status among cancer types, identifies subset of patients who may benefit from immunotherapy
Microsatellite instability (MSI) is a clonal change in the number of repeated DNA nucleotide units in microsatellites (DNA elements composed of repeating motifs that occur as alleles of variable lengths), and arises in tumours with deficient mismatch repair (MMR) due to the inactivation of one of the MMR genes.1 MSI is most commonly found in colon and endometrial cancers; however, recent findings have shown MSI to be a generalised cancer phenotype in as many as 24 cancer types.2 Evidence has recently revealed the ability of MSI to predict response of solid tumours to the anti-PD-L1 (programmed death ligand 1) agent pembrolizumab3, leading to the first tumour-agnostic drug approval by the USA’s Food and Drug Administration.4
Polymerase chain reaction (PCR) by fragment analysis (FA) is the current gold standard for detecting MSI. This isn’t always feasible or possible to perform in the clinic, however, as FA requires samples of both tumour and normal tissue. MMR deficiency is typically determined from immunohistochemistry (IHC). Both of these analyses are stand-alone tests and would be inefficient to perform on every patient with cancer given the low incidence of MSI among cancer types.2,5
This retrospective study, based on available data from Caris Life Sciences’ laboratory, showed the development of an MSI assay by Next-Generation Sequencing (MSI-NGS). DNA was sequenced with the NextSeq platform using the 592-gene NGS panel, and 7,317 microsatellite loci were examined. 2,189 cases were examined by PCR-FA and NGS. MSI-H was detected in 23 out of 26 cancer types. MSI-NGS, when compared with PCR-FA for all cancer types, had a sensitivity of 95.8%, specificity of 99.4%, positive predictive value (PPV) of 94.5% and a negative predictive value (NPV) of 99.2%.2
An additional comparison involved 1,986 cases examined by both MSI-NGS and by IHC for MMR protein status. Compared with MMR-IHC, NGS had a sensitivity of 87.1%, specificity of 99.6%, PPV of 95.5%, and NPV of 98.8%. The sensitivity (91.7%), specificity (99.7%), PPV (94.8%) and NPV (99.4%) were higher for NGS of colorectal cases.2
11,348 patients were examined to explore the relationship of MSI with PD-L1 and the total mutation burden (TMB was calculated based on the number of nonsynonymous somatic mutations identified by NGS, excluding any known single nucleotide polymorphisms). Notably, these cases were generally from patients with advanced, refractory disease who lacked obvious treatment options (a potential source of selection bias). The overall rates of MSI-H, TMB-high and PD-L1 positivity were 3.0%, 7.7% and 25.4%, respectively. 30% of MSI-H cases were TMB-low, and only 26% of MSI-H cases were PD-L1 positive.2 Notably, MSI-H cases that were not TMB-H or PD-L1 positive occurred in considerable percentages of ovarian (24%), neuroendocrine (57%), and cervical (33%) cancers.2
This study has demonstrated that MSI-NGS is comparable to the gold standard PCR-FA for determining MSI status across cancer types. Furthermore, MSI-NGS can reveal patients with MSI-H disease, but low TMB and no PD-L1 expression. With the recent approval of pembrolizumab for MSI-H patients of any solid tumour type, those patients lacking satisfactory treatment options can benefit from a potentially promising treatment that would not have been identified using either of the other two immunotherapy assays, PCR-FA and MMR-IHC.2
- MSI-H was detected in 23 out of 26 cancer types using MSI-NGS and PCR-FA.
- When compared with PCR-FA, MSI-NGS had a sensitivity of 95.8%, a specificity of 99.4%, positive predictive value of 94.5%, and a negative predictive value of 99.2%.
- MSI-NGS assay had only 87.1% sensitivity for MMR deficiency detection compared with MMR-IHC. Until more data are available, the best choice may be to run both MSI-NGS and MMR-IHC in lineages where MMR-IHC loss is more common to identify as many patients as possible.
- MSI-NGS revealed a subset of patients with MSI-H disease, but low TMB and no PD-L1 expression. These patients would not have been identified using either PCR-FA or MMR-IHC, and may benefit from the recently approved immunotherapy agent, pembrolizumab.
- de la Chapelle A, Hampel H. Clinical relevance of microsatellite instability in colorectal cancer. J Clin Oncol. 2010;28(20):3380-7. [URL]
- Vanderwalde A, Spetzler D, Xiao N, et al. Microsatellite instability status determined by next-generation sequencing and compared with PD-L1 and tumor mutational burden in 11,348 patients. Cancer Med. 2018;7(3):746-756. [PDF]
- Keytruda: Summary of efficacy in patients with advanced MSI-H/dMMR cancers [online]. Merck Sharp & Dohme Corp.; 2018 [cited May 2018]. Available from: [URL]
- FDA approves first cancer treatment for any solid tumour with a specific genetic feature [online]. U.S. Food and Drug Administration; 2017 [cited May 2018]. Available from: [URL]
- Le DT, Durham JN, Smith KN, et al. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science. 2017;357(6349):409-413. [URL]