TrueMark™ MSI Assay - FAQs

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.

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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.

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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.

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

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You may find the TrueMark MSI Assay User Guide here: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018868_MSI%20Assay_UG.pdf

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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

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The TrueMark MSI Assay Analysis Software is free and may be downloaded here: thermofisher.com/msisoftware

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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.

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The TrueMark MSI Assay has only been tested with FFPE samples at this time.

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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.

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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.

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The ABI marker sequences are proprietary and confidential.

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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.]

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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.

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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)

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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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

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).

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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

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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.

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