Table 3 Summary of PCR-based MSI testing systems.

From: Detecting mismatch repair deficiency in solid neoplasms: immunohistochemistry, microsatellite instability, or both?

Method

Microsatellite markers

Paired normal

Marker amplification

Readout strategies

TAT

Advantages

Limitations

NCI/Bethesda PCR-MSI testing1,5

BAT-25, BAT-26, D5S346, D2S123, D17S250

Yes

Fluorescent multiplex PCR

CE

~10 h

- Well-studied

- Established for CRC

- Lower sensitivity compared to newer panels

OncoMateTM MSI Dx Analysis System (Promega*)50

BAT-25, BAT-26, MONO-27, NR-21, NR-24; Penta C and Penta D (for sample authentication)

Yes

Fluorescent multiplex PCR

CE

10 h

- Quasi-monomorphic markers

- Better performance than NCI/Bethesda panel and considered a “gold standard”

- LOD 15%, FFPE tissue volume: 0.1–2.0 mm3

- Intended for CRC

IdyllaTM MSI Assay (Biocartis†)72

ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, SULF2

No

Real-time (RT) PCR

HRM

2.5 h

- Cross-ethnicity monomorphic markers

- LOD 10%, FFPE tissue volume: 0.25–3.0 mm3

      

- High concordance with IHC and other MSI tests for CRC

- Automated from loading of FFPE to reporting, hands on time <2 min

- Intended for CRC

- Lower sensitivity for non-CRC tumor types (e.g., endometrial cancers showing MSH6d8)

  1. CE capillary electrophoresis, CRC colorectal cancer, FFPE formalin-fixed paraffin-embedded, HRM high resolution melting analysis, IHC immunohistochemistry, LOD limit of detection, MSH6d MSH6 deficient, MSI microsatellite instability, NCI National Cancer Institute, PCR polymerase chain reaction, TAT turnaround time.
  2. *OncoMateTM MSI Dx Analysis System, formerly MSI Analysis System (Promega, Madison, WI, USA).
  3. †IdyllaTM MSI Assay (Biocartis, Mechelen, Belgium).
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