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Applied Biosystems™ TrueMark™ MSI Assay

Catalog No. A45295
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Description

The Applied Biosystems™ TrueMark MSI Assay is a low-input, single-amplification solution for the rapid identification of microsatellite instability (MSI) in formalin-fixed paraffin-embedded (FFPE) samples from multiple tumor tissue types for research applications.

The Applied Biosystems TrueMark MSI Assay leverages an expanded 6-dye set to incorporate additional markers and does not require the use of a tumor-normal match, thereby cutting in half the number of wells required for each sample, as well as reducing the sample handling burden. The assay is compatible with the Applied Biosystems SeqStudio and 3500 Series genetic analyzers.

MSI analysis software

The associated TrueMark MSI Analysis Software (included at no additional charge) is designed specifically for the TrueMark MSI Assay to enable automated calling of markers and samples, offering greater ease of analysis by reducing the manual QC, analysis, and review required to determine sample status. The automated calling functions without the use of a tumor-normal match, but it is also compatible with tumor-normal pairs.

The TrueMark MSI Assay features include:

  • Expanded coverage - 13 MSI markers
    • BAT-25, BAT-26, BAT-40, CAT-25, NR-21, NR-22, NR-24, NR-27 (publicly known MSI markers)
    • ABI-16, ABI-17, ABI-19, ABI-20A, ABI-20B (MSI markers proprietary to Thermo Fisher Scientific)
    • PentaD, TH-01 (sample ID markers)
  • Optional normal control - no requirement for use of tumor-normal match for interpretation
  • Low input - use as little as 2 ng FFPE-derived DNA
  • Automated calling - analysis software includes automated calling of markers and samples to accelerate initial data interpretation
  • Simple analysis software - streamline QC, analysis, and review of samples

Analysis software for download

  • TrueMark MSI Analysis Software

Supplied reagents

  • TrueMark MSI Primer mix
  • TrueMark MSI Master mix
  • TrueMark MSI No Template Control
  • TrueMark MSI Amplification Control

Required reagents not supplied in the TrueMark MSI Assay

  • GeneScan 600 LIZ Size Standard v2.0
  • Hi-Di Formamide
  • DS-36 Matrix Standard (Dye Set J6)

The TrueMark MSI Assay has been tested with RecoverAll Total Nucleic Acid Isolation Kit for FFPE and Qiagen QIAamp™ DSP DNA FFPE Tissue Kit for sample preparation. Please note these are not included in the kit.

TRUSTED_SUSTAINABILITY

Specifications

Content And Storage • TrueMark MSI Assay Master Mix
• TrueMark MSI Assay Primer Mix
• TrueMark MSI Assay Amplification Control
• TrueMark MSI Assay No-Template Control

Store at -15 to -25°C, then 2–8°C after first use.
For Use With (Application) Sequencing
No. of Reactions 100
Product Line TrueMark
Product Type MSI Assay
Shipping Condition Dry Ice
Test Type Oncology

Frequently Asked Questions (FAQs)

Can I freeze TrueMark MSI Assay (Cat. No. A45295) after my initial use?

We recommend storing TrueMark MSI Assay in the refrigerator after initial use because there are a lot of dye-labeled primers in the mix. Freeze-thaws could cause the dye to break down.
Can I use GeneMapper Software to analyze data generated with the TrueMark MSI Assay?

TrueMark MSI Assay data can be analyzed in GeneMapper Software, but a tumor-normal match must be run and there is no automated calling. We recommend using the full solution for the TrueMark MSI Assay which includes the new TrueMark MSI Assay Analysis Software.
Can I use the TrueMark MSI Assay Analysis Software with any other MSI kits from other known vendors or with an MSI assay that I develop myself?

No, the TrueMark MSI Assay Analysis Software is designed exclusively for use with and custom designed around the panel used in our TrueMark MSI Assay.
Where can I find the TrueMark MSI Assay Quick Reference Guide?

You may find the TrueMark MSI Assay Quick Reference Guide here: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018869_MSI%20Assay_QR.pdf
Where can I find the TrueMark MSI Assay User Guide?

You may find the TrueMark MSI Assay User Guide here: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018868_MSI%20Assay_UG.pdf
Where can I find the TrueMark MSI Assay Analysis Software Version 1.0 User Guide?

You may find the TrueMark MSI Assay Analysis Software v1.0 User Guide here: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018874_TrueMarkMSAnalysisSoftware_UG.pdf
How can I get the TrueMark MSI Assay Analysis Software?

The TrueMark MSI Assay Analysis Software is free and may be downloaded here: thermofisher.com/msisoftware
What size standard do you recommend using with the TrueMark MSI Assay?

The GeneScan 600 LIZ dye Size standard v2.0 (Cat. No. 4408399) must be used with the TrueMark MSI Assay Analysis Software, and it has to be ordered separately.
Does the sample input for the TrueMark MSI Assay need to be FFPE samples or can I use blood (cfDNA)?

The TrueMark MSI Assay has only been tested with FFPE samples at this time.
Do you recommend running a tumor-normal pair sample or tumor sample only with the TrueMark MSI Assay?

The TrueMark MSI assay was developed with the aim of not requiring a normal control. The sensitivity is comparable to running both a normal sample with the matched tumor sample. In order to detect MSI events at very low abundance (for example, if the pathogenic cells make up only a very small fraction of a biopsy), concurrently running a normal control will solidify the accuracy of the calls and increase the analytical sensitivity of the assay.
How did you choose the markers that are included in the TrueMark MSI Assay?

The markers for the TrueMark MSI Assay were chosen from literature/publications and bioinformatically determined from GWAS (genome-wide association studies) to be quasi-monomorphic and sensitive across multiple cancer types.

What are the sequences of the ABI markers used in the TrueMark MSI Assay?

The ABI marker sequences are proprietary and confidential.
What is considered "MSI-High" in the TrueMark MSI Assay analysis?

We use the following cut-offs based on the paper cited below:
- If >30% of markers show instability, the overall sample is called as MSI-H;
- If <30% of markers show instability, the overall sample is called MSI-L
- If 0% of markers show instability, the overall sample is called MSS
These are the default settings, but you may choose to adjust the percentages.

[Paper citation: Cicek, M et al (2011) Quality Assessment and Correlation of Microsatellite Instability and Immunohistochemical Markers among Population- and Clinic-Based Colorectal Tumors. The Journal of Molecular Diagnostics (13)3.]
What are the sample ID markers used in the TrueMark MSI Assay?

The sample ID markers in the TrueMark MSI Assay are PentaD and TH-01; they are included to detect whether there have been any mistakes in the sample handling process.
Which markers are included in the TrueMark MSI Assay?

The TrueMark MSI Assay contains 13 MSI markers:
--BAT-25, BAT-26, BAT-40, CAT-25, NR-21, NR-22, NR-24, NR-27 (publicly known MSI markers)
--ABI-16, ABI-17, ABI-19, ABI-20A, ABI-20B (MSI markers proprietary to Thermo Fisher Scientific)
--PentaD and TH-01 (Sample ID markers)
How do I analyze data generated using the TrueMark MSI Assay?

Data generated using the TrueMark MSI Assay is meant to be analyzed with TrueMark MSI Analysis Software (downloadable from thermofisher.com/msisoftware). Alternatively, you may use GeneMapper Software (v5.0 or later), but a tumor-normal match must be run and there is no automated calling. We recommend using the full solution for the TrueMark MSI Assay that includes the new TrueMark MSI Assay Analysis Software.
What are the shipping/storage conditions/shelf life for the TrueMark MSI Assay?

The TrueMark MSI Assay (Cat. No. A45295) is shipped on dry ice and should be stored at -25 degrees C to -15 degrees C until first use. After the first use, the components should be stored at 2-8 degrees C. The assay is guaranteed stable for ≤6 months or until the expiration date (whichever comes first).
What are the components of the TrueMark MSI Assay?

The TrueMark MSI Assay (Cat. No. A45295) contains 4 tubes:
- TrueMark MSI Assay Master Mix
- TrueMark MSI Assay Primer Mix
- TrueMark MSI Assay Amplification Control
- TrueMark MSI Assay No-Template Control

What is the TrueMark MSI Assay?

The TrueMark MSI Assay (Cat. No. A45295) is a low-input, single-amplification solution for the rapid identification of microsatellite instability (MSI) in formalin-fixed paraffin-embedded (FFPE) samples from multiple tumor tissue types for research applications. It uses a 6-dye (J6) dye set, the DS-36 Matrix Standard (Dye Set J6) (Cat. No. 4425042) and is compatible with the SeqStudio and 3500 Series genetic analyzers.

Safety and Handling

WARNING: Reproductive Harm - www.P65Warnings.ca.gov

For Research Use Only. Not for use in diagnostic procedures.

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