Clinical Testing for Mismatch Repair in Neoplasms Using Multiple Laboratory Methods

Abstract

Background: A deficiency in DNA mismatch repair function in neoplasms can be assessed by an immunohistochemical (IHC) analysis of the deficiency/loss of the mismatch repair proteins (dMMR) or by PCR-based methods to assess high microsatellite instability (MSI-H). In some cases, however, there is a discrepancy between the IHC and MSI analyses. Several studies have addressed the issue of discrepancy between IHC and MSI deficiency assessment, but there are limited studies that also incorporate genetic/epigenetic alterations. Methods: In this single-institution retrospective chart-review study, we reviewed 706 neoplasms assessed between 2015 and 2021. All eligible neoplasms were assessed by IHC testing, MSI analysis by PCR-based assay, and tumor-normal paired next-generation sequencing (NGS) analysis. Eighty percent of neoplasms with MLH1 protein loss had a concurrent MLH1 promoter methylation analysis. Mutation data for MMR genes, IHC, MSI analysis, and tumor histology were correlated with each other. Results: Fifty-eight (8.2%) of 706 neoplasms had MSI-H by PCR and/or dMMR by IHC. Of the 706 analyzed neoplasms, 688 neoplasms (98%) had concordant results: MSI-H/dMMR (n = 44), microsatellite-stable (MSS)/proficient MMR (pMMR) (n = 625), and MSI-Low (L)/pMMR (n = 19). Of the remaining 18 neoplasms, 9 had a major discordance: MSS/loss of MSH2 and MSH6 (n = 3), MSS/loss of MSH6 (n = 2), MSS/Loss of MLH1 and PMS2 (n = 1), and MSI-High/pMMR (n = 3). In total, 57% of cases with dMMR and 61% of cases with MSI-H had a null mutation of an MMR gene mutation (or methylation of the MLH1 promoter), whereas this figure was 1% for neoplasms with a normal IHC or MSI pattern (p < 0.001). Among 9 cases with major discordance between MSI and IHC, only 3 cases (33%) had an underlying genetic/epigenetic etiology, whereas 37 (76%) of 49 cases with MSI-H and/or dMMR and without major discordance had an underlying genetic abnormality (p = 0.02). Discussion: For most neoplasms, IHC and PCR-based MSI testing results are concordant. In addition, an underlying genetic abnormality (a null mutation of an MMR gene or MLH1 promoter methylation) was attributable to dMMR and/or MSI-H findings. For neoplasms with major discordance in IHC and MSI testing, the addition and integration of NGS results and MLH1 promoter methylation analyses can be beneficial for resolving borderline cases, thereby facilitating patient management.

Real-world study on microsatellite instability and mismatch repair deficiency testing patterns among patients with metastatic colorectal cancer in Spain

“…The prevalence of dMMR in patients with CRC is higher in early stages than in advanced disease, and higher in western populations [ 25 , 26 ]. The prevalence in our study (6%) overlaps with that reported in two recent series in real-world practice in the US using the Veterans Affairs Health Care System [ 27 ] and the MD Anderson Cancer Center [ 28 ] databases. It is also within the range shown in a recent review that included a pooled analysis [ 26 ].…”

Intragenic EGFR::EGFR.E1E8 Fusion (EGFRvIII) in 4331 Solid Tumors

“…The genomic tumor DNA was extracted and purified using AllPrep kit on a QIAcube liquid handling platform (Qiagen, Germantown, MD, USA) [ 23 ]. The peripheral blood DNA (a default source of germline DNA received in an EDTA tube) was extracted and purified using a Maxwell RSC Blood DNA Kit (Promega, Madison, WI, USA) [ 24 ].…”

Testing for deficient mismatch repair and microsatellite instability

“…2 and 4 ). To further rule out MLH1 involvement, additional BRAF (for CRC) and/or MLH1 promoter methylation analysis for other tumor entities should be considered if necessary [ 20 , 33 ]. Isolated loss of MSH6 has also been described for rectal cancer after chemoradiation [ 3 , 8 ], although this is typically not associated with MSI‑H.…”

“…Supplementary molecular testing should be performed for further clarification of MMR-IHC findings that are ambiguous or unusual. MLH1 promoter methylation testing (or BRAF mutation testing for CRC; [ 33 ]) and NGS analysis of the tumor may be useful in clarifying the MMR gene mutation status. However, microsatellite analysis by NGS should be validated for each organ system against MMR-IHC and MSI-PCR as the reference method [ 10 , 11 , 28 ].…”