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Qualitative and Quantitative Aspects of Discrepancies between Various Methods for Microsatellite Instability Detection

Balkan Journal of Medical Genetics
Volume 28 (2025): Issue 1 (June 2025)
By:
Open Access
|Oct 2025

Figures & Tables

Figure 1.

Distribution of MSI patients by various methods for MSI detection. Classical MMR deficiency = detected by both MSI-PCR and IHC (MSI-H and loss of MMR proteins). Unusual MMR deficiency = detected by one method, MSI-PCR or IHC: type 1 (MSI-H with intact MMR protein expression) and type 2 (MSS and isolated loss of PMS2 or MSH6). *Clinically and molecularly diagnosed Lynch syndrome (pathogenic mutation in the MSH6) with MSS status, normal expression of all four MMR proteins and negative MSI-NGS result. MSI, microsatellite instability, MSS, microsatellite stability, NGS, next-generation sequencing, dMMR, deficient mismatch repair, pMMR, proficient mismatch repair, IHC, immunohistochemistry, PCR, polymerase chain reaction
Distribution of MSI patients by various methods for MSI detection. Classical MMR deficiency = detected by both MSI-PCR and IHC (MSI-H and loss of MMR proteins). Unusual MMR deficiency = detected by one method, MSI-PCR or IHC: type 1 (MSI-H with intact MMR protein expression) and type 2 (MSS and isolated loss of PMS2 or MSH6). *Clinically and molecularly diagnosed Lynch syndrome (pathogenic mutation in the MSH6) with MSS status, normal expression of all four MMR proteins and negative MSI-NGS result. MSI, microsatellite instability, MSS, microsatellite stability, NGS, next-generation sequencing, dMMR, deficient mismatch repair, pMMR, proficient mismatch repair, IHC, immunohistochemistry, PCR, polymerase chain reaction

Figure 2.

Quantitative MSI-NGS levels of patients with sporadic and Lynch Syndrome-associated CRC or endometrial cancers in relation to different types of MMR deficiencies, affected genes, and localization.The threshold level for NGS-MSI positivity is set at 3.5%. MSI, microsatellite instability, MMR, mismatch repair, IHC, immunohistochemistry, VUS, variant of uncertain significance, CRC, colorectal cancer, EC, endometrial cancer
Quantitative MSI-NGS levels of patients with sporadic and Lynch Syndrome-associated CRC or endometrial cancers in relation to different types of MMR deficiencies, affected genes, and localization.The threshold level for NGS-MSI positivity is set at 3.5%. MSI, microsatellite instability, MMR, mismatch repair, IHC, immunohistochemistry, VUS, variant of uncertain significance, CRC, colorectal cancer, EC, endometrial cancer

Figure 3.

Proposed strategy for more accurate cost-effective evaluation of MMR deficiency and potential subsequent NGS-MSI testing for quantitative assessment.IHC, immunohistochemistry, LS, Lynch syndrome, dMMR, deficient mismatch repair, pMMR, proficient mismatch repair, MSI, microsatellite instability, MSS, microsatellite stability, NGS, nextgeneration sequencing
Proposed strategy for more accurate cost-effective evaluation of MMR deficiency and potential subsequent NGS-MSI testing for quantitative assessment.IHC, immunohistochemistry, LS, Lynch syndrome, dMMR, deficient mismatch repair, pMMR, proficient mismatch repair, MSI, microsatellite instability, MSS, microsatellite stability, NGS, nextgeneration sequencing

Clinical and molecular data of the patients included in the study

Cancer typeMMR deficiency typeMSI/IHC statusID numberSexAgeTumor localization*Affected geneDNA (protein) change**Molecular defectMLH1 methylationÌSI-PCRIHCMSI-NGS
MLH1MSH2MSH6PMS2
HereditaryClassical MMR deficiency (n=16)MSI+ IHC+H1F43proximal CRCMLH1c.896_897insC (p.Pro300SerfsTer7)deletion out-of-frame−+X X
H2F60proximal CRCMLH1c.392C>G (p.Ser131Ter)nonsense mutation−+X X
H3F57proximal CRCMLH1c.683T>C (p.Leu228Pro)missense mutation−+X X49,3
H4F41proximal CRCMLH1c.1667+1del (p.?)splice site mutation−+X X74
H5M15proximal CRCMSH2c.2211-2A>C (p.?)splice site mutation−+ XX
H6M50proximal CRCMSH2c.2211-2A>C (p.?)splice site mutation−+ XX
H7F63proximal CRCMSH2c.1786_1788delAAT (p.Asn596del)deletion in-frame−+ XX
H8M46distal CRCMSH2c.1786_1788delAAT (p.Asn596del)deletion in-frame−+ XX
H9M41distal CRCMSH2c.209_211+11del (p.?)deletion in-frame−+ XX
H10F27proximal CRCMSH2c.1012 G>A (p.Gly338Arg)missense mutation−+ XX 56,5
H11F52distal CRCMSH6c.3991C>T, (p.Arg1331Ter)nonsense mutation−+ X 50
H12F48endometrialMSH6:c.3172G>C (p.Asp1058His)missense mutation−+ X 36
H13M40distal CRCMSH6c.3263delT (p.Phe1088SerfsTer2)deletion out-of-frame−+ X 42,9
H14M41proximal CRCPMS2g.(5984924_5987848)_ (6015520_?)del (p.?)large deletion−+ X
H15M68distal CRCPMS2c.2192_2196delTAACT (p.Leu731CysfsTer3)deletion out-of-frame−+ X73,5
H16M65proximal CRCPMS2c.1321_1322delA (p.Arg443GlufsTer5)deletion out-of-frame++X X
Unusual MMR deficiency (n=9)Type1 MSI+IHC-H17M55proximal CRCMLH1c.244A>G (p.Thr82Ala)missense mutation−+ 54
H18M51proximal CRCMLH1c.244A>G (p.Thr82Ala)missense mutation−+ 53,8
H19M38proximal CRCMLH1c.62C>T (p.Ala21Val)missense mutation−+ 43
H20F37distal CRCMSH6c.2927G>C (p.Arg976Pro)missense mutation−+ 40
Type2 MSI-IHC+H21F52endometrialMSH6c.900_901insTC (p.Lys301SerfsTer5)insertion out of frame+−/ X/ XX/ X12
H22F41endometrialMSH6c.3514dupA (p.Arg1172LysfsTer5)deletion out-of-frame−− X 4,3
H23F45distal CRCPMS2c.2437C>T (p.Arg813Trp)missense mutation-VUS−− X1,7
H24F44distal CRCMSH6c.2384T>C (p.Ile795Thr)missense mutation-VUS−− X 1,16
H25M51proximal CRCMSH6c.1151_1156dupGGAGGC (p.Arg384_385dup)Insertion in-frame - VUS−− X 2
pMMR (n=1)MSI-IHC-H26F44distal CRCMSH6c.457+1G>T (p?)splice site mutation−− 3,12
SporadicClassical MMR deficiency (n=18)MSI+ IHC+S1M54proximal CRCMLH1NApromoter methylation++X X79,5
S2M39distal CRCMLH1NApromoter methylation++X X73,7
S3M72distal CRCMLH1NApromoter methylation++X X
S4F57endometrialMLH1NApromoter methylation++X X56,5
S5F57distal CRCMLH1NApromoter methylation++X X47,9
S6M73distal CRCMLH1NApromoter methylation++X X76,1
S7F75endometrialMLH1NApromoter methylation++X X
S8F73endometrialMLH1NApromoter methylation++X X19,9
S9F53endometrialMLH1NApromoter methylation++X X19,2
S10M57distal CRCMLH1NApromoter methylation++X X9,1
S11M68distal CRCMLH1NApromoter methylation++X X4,4
S12F60distal CRCMLH1NApromoter methylation++X X41,1
S13F58proximal CRCMLH1NApromoter methylation++X X77,9
S14M67proximal CRCMLH1NApromoter methylation++X X76,7
S15M72proximal CRCMLH1NApromoter methylation++X X48,9
S16M77proximal CRCMLH1NApromoter methylation++X X64,3
S17F68proximal CRCMLH1NApromoter methylation++X X52,8
S18F78distal CRCMLH1NApromoter methylation++X X
DOI: https://doi.org/10.2478/bjmg-2025-0009 | Journal eISSN: 2199-5761
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Language: English
Published on: Oct 8, 2025
Published by: Macedonian Academy of Sciences and Arts
In partnership with: Paradigm Publishing Services
Publication frequency: 2 times per year
Related subjects:
Medicine,
Basic medical science,
Basic medical science, other

© 2025 M Staninova-Stojovska, N Matevska-Geshkovska, E Krstevska-Bozhinovikj, R Jovanovic, K Kubelka Sabit, B Angelovska, N Mitreski, P Noveski, A Dimovski, published by Macedonian Academy of Sciences and Arts
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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