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Table 1 Comparison of different assays used to detect mismatch repair defects and other predictors of immune therapy response or resistance

From: Neoantigens and genome instability: impact on immunogenomic phenotypes and immunotherapy response

Technique or assay Description Attributes Deficiencies
MSI-PCR PCR-based amplification of known microsatellite loci, gel electrophoresis, and software scoring to detect instability as a multiple-band pattern in amplicons Focused test with rapid turn-around time Interpretation difficulties, limited to MSI diagnosis, no information on genetic source of MMRd
dMMR/IHC Antibody-based staining of FFPE sections from tumor, followed by microscopic examination and scoring to detect MMR proteins (MSH2, MSH6, MLH1, PMS2) Focused test using a conventional pathology approach, inexpensive, rapid turn-around time Evaluates the end result of MMR protein depleting alterations only, subject to inter-individual interpretation
CIN/FISH Hybridization of centromere-specific fluorescent probes to chromosomal spreads, microscopic scoring of centromeric counts to detect aneuploidy Genome-wide evaluation of chromosomal instability Counting-based evaluation that is subject to inter-individual interpretation variability
MMR/MSI-NGS panel NGS of genes for MMR proteins, mutation detection and annotation of pathogenic variants Focused evaluation of mutations across known MMRd genes Insensitive to large-scale alterations such as CNVs, insufficient breadth for TMB or neoantigen prediction
NGS/WES NGS of all known coding exons of genes, mutation detection and annotation of pathogenic variants in genes Unbiased evaluation of mutations across all coding genes, MSI evaluation (added probes), neoantigen prediction, TMB enabled Mutational signature calculation may be compromised by lack of breadth
NGS/WGS NGS of whole genome libraries from cancer and matched normal DNA, comprehensive variant detection, and annotation of variants Unbiased evaluation of mutations across all coding genes, MSI evaluation, neoantigen prediction, TMB, mutational signature enabled Expensive to generate sufficient coverage from low cellularity tumors
  1. CIN chromosomal instability, CNV copy number variant, dMMR deficient mismatch repair, FFPE formalin-fixed paraffin-embedded, FISH fluorescence in situ hybridization, IHC immunohistochemistry, MMR mismatch repair, MMRd mismatch repair defect, MSI microsatellite instability, NGS next generation sequencing, TMB tumor mutational burden, WES whole exome sequencing, WGS whole genome sequencing