Key Features



Limit of detection down to 1% VAF

Accurate results with as little as 3ng input DNA


User Friendly

Matched normal not required

Included software reports MSI-H, MSI-L/MSS


Fast Turnaround

Results in less than two hours

Batch up to 47 samples per qPCR run



Compatible with tumor tissue or cell-free DNA (cfDNA)


For research use only. Not for use in diagnostic procedures.

The VarTrace Microsatellite Instability (MSI) Assay enables highly sensitive detection of MSI. This assay is intended for the qualitative detection of mutations in five MSI loci without the need of matched normal.

NuProbe’s VarTrace MSI Assay utilizes patented BDA technology to selectively amplify the alleles from MMR deficient samples enabling detection of MSI high (MSI-H) status with a limit of detection to 1% variant allele frequency (VAF). The assay interrogates five mononucleotide markers (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) to determine MSI status for each sample.

Microsatellite Instability Markers Covered

BAT-25, BAT-26, NR-21, NR-24, and MONO-27

Sample Data

  • Limit of Detection Performance
  • VarTrace MSI assay shows superb analytical limit of detection down to 1% allele frequency of the MSI unstable molecules.
  • MSI Determination
  • The MSI status is based on the Ct values for each marker in the sample, by comparing with the GAPDH internal control to normalize the sample input. If the Ct value of marker is earlier than threshold, the marker is a positive. And based on the number of positive markers out of the 5 markers, we can call the sample MSI-H (>2/5); MSI-L(1/5) or MSS(0/5).
  • MSI Software
  • We provide an easy-to-use software to interpret MSI results and generate a report. Simply upload the qPCR data into the NuProbe MSI software, and the software gives sample results in a plate view map by color code. Users can then label the samples, view the result for each marker and qPCR curves, and export the MSI status report in excel format.
  • qPCR Data Curve
  • qPCR curve results from a colorectal cancer MSS sample and a colorectal cancer MSI sample.
  • Clinical Specimen Results
  • DNA from a single 5um FFPE section is enough for the VarTrace MSI assay.20 Origene repository colorectal cancer samples were tested using the VarTrace MSI assay. 3/20 MSI-H is consistent with expected percentage of MSI-H in colorectal cancer.


Step 1: DNA Extraction

DNA is extracted from clinical samples with commercial extraction kits such as cobas® cfDNA Sample Preparation Kit, QIAamp® DNA Blood Mini Kit, GeneRead® DNA FFPE Kit.

Sanger Sequencing Workflow

Step 2: qPCR BDA Reaction

NuProbe’s qPCR kit reagents and clinical samples are prepared for qPCR reactions. After running the reaction, Ct results are obtained.

1.5 hrs (15 min hands-on)

Computer Analysis Icon

Step 3: Results Interpretation

The MSI status of each sample will be visualized and reported by the easy-to-use VarTrace MSI software.

2 min hands-on

Compatible Instruments

BioRad CFX96

BioRad CFX96

The assay has been optimized with BioRad CFX96. To use other qPCR instruments, please contact us.


NuProbe Kit Box
Catalog Number

48 Reactions

Technologymulti-blocker mBDA & qPCR
Kit size48 specimens / kit
BiomarkersTube 1: BAT26, NR21, NR24
Tube 2: BAT25, Mono27
Internal ControlGAPDH
Tubes/wells per specimen2
Turnaround timeqPCR only: 1h30min including 5min hands-on time
Limit of detection≥ 10ng per reaction: 1%
< 10ng per reaction: 5%
Specificity>98% at 1% VAF
Specimen typeBlood or FFPE
Specimen input1.5-15 ng per reaction (3-30 ng per specimen) ideally 20ng (10 ng per tube)
ControlPositive (5%) and Negative
Amplicon length[80, 120] bp
Storage condition-20°C, up to 6 months
InstrumentsBioRad CFX96
SoftwareIncluded software reports MSS, MSI-L, MSI-H based on N/5 abnormal

Request Quote / Demo

Yan Helen Yan, Ph.D., senior research scientist at NuProbe. She obtained her Doctorate degree from Rice University and has over 7 years of research experience in nucleic acid diagnostics, genomics, qPCR and next-generation sequencing. Contact Helen for questions about the VarTrace MSI assay.

    Quantity (if requesting a quote)