Analysis of Concordance Between Next-Generation Sequencing Assessment of Microsatellite Instability and Immunohistochemistry-Mismatch Repair From Solid Tumors

Abstract

Purpose: The new CAP guideline published in August 2022 recommends using immunohistochemistry (IHC) to test for mismatch repair defects in gastroesophageal (GE), small bowel (SB), or endometrial carcinoma (EC) cancers over next-generation sequencing assessment of microsatellite instability (NGS-MSI) for immune checkpoint inhibitor (ICI) therapy eligibility and states there is a preference to use IHC over NGS-MSI in colorectal carcinoma (CRC).

Methods: We assessed the concordance of NGS-MSI and IHC-MMR from a very large cohort across the spectrum of solid tumors.

Results: Of the over 190,000 samples with both NGS-MSI and IHC-MMR about 1,160 were initially flagged as discordant. Of those samples initially flagged as discordant, 50.9% remained discordant after being reviewed by an additional pathologist. This resulted in a final discordance rate of 0.31% (590/191,767). Among CRC, GE, SB and EC, 55.4% of mismatch repair proficient/MSI high (MMRp/MSI-H) tumors had at least one somatic pathogenic mutation in an MMR gene or POLE. Mismatch repair deficient/microsatellite stable (MMRd/MSS) tumors had a significantly lower rate of high tumor mutational burden than MMRp/MSI-H tumors. Across all solid tumors, MMRd/MSI-H tumors had significantly longer overall survival (OS; hazard ratio [HR], 1.47, P < .001) and post-ICI survival (HR, 1.82, P < .001) as compared with MMRp/MSS tumors. The OS for the MMRd/MSS group was slightly worse compared to the MMRp/MSI-H tumors, but this difference was not statistically significant (HR, 0.73, P = .058), with a similar pattern when looking at post-ICI survival (HR, 0.43, P = .155).

Conclusion: This study demonstrates that NGS-MSI is noninferior to IHC-MMR and can identify MSI-H tumors that IHC-MMR is unable to detect and conversely IHC-MMR can identify MMRd tumors that NGS-MSI misses.

FIG 1.

(A) H&E, (B) MLH1, and (C) PMS2 at 10× magnification showing an EC tumor with loss of nuclear expression for MLH1 and PMS2. This tumor was MMRd/MSI-H. EC, endometrial carcinoma; H&E, hematoxylin and eosin; MMRd, mismatch repair deficient; MSI-H, microsatellite instability.

FIG 2.

Oncoprint of MMRp/MSI-H tumors with at least one of the eight investigated mutations. For Group 1 mutations, positive indicates a pathogenic missense mutation and negative indicated no pathogenic missense mutation. For Group 2 and POLE Mutant, positive indicates any pathogenic mutation and negative indicates no pathogenic mutations. CRC, colorectal carcinoma; EC, endometrial carcinoma; GE, gastroesophageal; MMRp, mismatch repair proficient; MSI-H, microsatellite instability high; SB, small bowel.

FIG 3.

(A) TMB-H prevalence for the four investigated tumor types. (B) Prevalence of TMB-H for discordant and concordant CRC tumors (q < 0.05 as indicated by asterisk for both). (C) Difference in immune cell infiltrate between MSS/MMRd and MSI-H/MMRp tumors in three cancer groups (P < .05 denoted by black asterisk, q > 0.05 for all immune cell population comparisons). CRC, colorectal carcinoma; EC, endometrial carcinoma; GE, gastroesophageal; MMRd, mismatch repair deficient; MMRp, mismatch repair proficient; MSS, microsatellite stable; MSI-H, microsatellite instability high; SB, small bowel; TMB, tumor mutational burden.

FIG 4.

Overall survival (A, C) and time from immune checkpoint inhibitor to last contact (B, D) for concordant MMRd/MSI-H tumors as compared with MMRp/MSS (A, B) and discordant MMRp/MSI-H and MSS-MMRd tumors (C, D). Tumors included in this analysis are a subset of those in the main text who had matched insurance claim data available. HR was calculated using the Cox proportional hazards model, and P values were calculated using the log-rank test. HR, hazard ratio; ICI, immune checkpoint inhibitor; MMRd, mismatch repair deficient; MMRp, mismatch repair proficient; MSS, microsatellite stable; MSI-H, microsatellite instability high; OS, overall survival.