Microsatellite instability (MSI) is a form of genomic instability due to reduced fidelity during the replication of repetitive DNA. Often occurring in tumor cells, MSI leads to the appearance of multiple alleles at microsatellite loci, which can be easily identified.

Microsatellite instability analysis involves comparing allelic profiles of specific microsatellite markers in normal and tumor samples. Data available for thousands of markers across numerous organisms makes microsatellite analysis a widely accepted tool for linkage and association studies as well as for identification studies of individual organisms (including human identification).

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Genomic Instability Identified by MSI Analysis

The electropherogram of the dinucleotide repeat marker D18S35 from a homozygous individual (top panel). The appearance of numerous extra alleles at lower molecular weights in the tumor sample (bottom panel) indicates significant genomic instability.

Step-by-Step Guide to Microsatellite Instability

DNA Purification kit

DNA extraction is a critical first step in the experimental workflow of DNA Sequencing and Fragment analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.

Recommended Products: DNA Isolation


Amplify microsatellite loci of interest by PCR using 5' fluorescent labeled primer.

Recommended Products: Design Primer & Perform PCR

Fragment Analysis sizing graph image.

Add aliquot of PCR product to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.

Recommended Products: Prepare Sample for Analysis

Sizing Information

To learn more about our GeneScan Size standards used in sizing experiments please see our table below.

When DNA sample fragments are labeled with: Choose a size standards labeled with: AB Dye Set: Possible Applications Other AB kits and products:
dR110, dR6G, dTAMRA™, dROX LIZ DS-02 SNaPshot® SNaPshot® primer focus kits, SNaPshot® Multiplex kits
5-FAM™, HEX™, NED™ ROX™ DS-30 Custom Fragment Analysis Custom Oligos
6-FAM™, VIC™, NED™ ROX™ DS-31

Custom Microsatellites

Custom Oligos
5-FAM™, JOE, NED™ ROX™ DS-32 Microsatellite (Forensic) AmpFISTR® Kits,
Plant/Microbial AFLP Kits®
6-FAM™, VIC™, NED™, PET® LIZ DS-33 Microsatellite (Forensic) AmpFISTR® Kits,
Custom Oligos
Capillary Electrophoresis

During capillary electrophoresis, the products of the PCR are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the fluorescent DNA fragments are separated by size and are detected by a laser/camera system.

Which Electrophoresis Instrument (Genetic Analyzer) Is Right for You?

Number of Capillaries 96 48 24 8 16 4 1
Compatible Applications:
(S) Supported; (A) AB Demonstrated; (C) Customer Demonstrated; (N) Not Supported
- Instability/RER A A A A A A A

Analyze the microsatellite profile. Appearance of numerous extra alleles in the microsatellite profile indicates a genome instability.

Which Data Analysis Software Is Right for You?

Highlighted Products for Microsatellite Instability Analysis:

Verti Thermal Cycler

3500 Series Genetic Analyzers

GeneMapper® Software

Visistat reference component