Dec 8, 2017




Clinical Hub,Tools & Resources,UWHC Lab Test Directory,Molecular Diagnostics

Microsatellite Instability

Microsatellite Instability (HCMSI) Molecular Diagnostics Lab Test

Name: Microsatellite Instability

Test Name: Microsatellite Instability

Health Link Test Code: HCMSI

CPT Code(s): 81301

Test Component:

Loci: BAT 25, BAT26, NR21, NR24 and NR27; Pentanucleotide repeats: PentaC and PentaD

Methodology: Real-Time PCR followed by Direct Sequencing

Clinical Information:

Approximately 15% of colorectal cancers (CRC) are caused by a defect in the DNA mismatch repair (MMR) pathway. A small fraction of these are due to germline mutations in at least one of several MMR genes; this is known as Lynch syndrome (LS) or nonpolyosis CRC (HNPCC). Individuals with HNPCC/LS have a much higher lifetime risk of CRC, as well as gastric, endometrial and other cancers. In addition to identifying families with Lynch syndrome, tumor chemosensitivity may depend on its MMR capability. Two main approaches can be used to screen a tumor for defects in the MMR pathway; one can look for the expression of MMR proteins by immunohistochemistry, or one can assess microsatellite instability (MSI). Microsatellites are tandem repeats found throughout the human genome. Their repetitive nature makes the DNA polymerase prone to slippage during DNA replication, but these errors are usually corrected by the MMR system. By monitoring the sizes (number of repeats) of several different microsatellites within a tumor, one can assess the function of the MMR pathway. An MMR defect will result in microsatellite (length) instability, or MSI. Due to the inherent limitations of each of these methods, the use of MSI and MMR protein IHC concurrently is recommended for the most effective screening of all new CRC patients for HNPCC/LS.


The UWHC MSI assay consists of five polymorphic loci of mononucleotide repeats that often vary in length between individuals. The markers used in the assay are NR21, NR24, NR27, BAT25, and BAT26. To screen for MSI, one compares tumor and normal tissue from the same patient, and looks for differences in the lengths of each of the five microsatellites between the two tissues. This is done by amplifying across each locus and including one primer that is labeled by a fluorophore. The fluorescently tagged amplicons are then separated by capillary electrophoresis. In addition to the polymorphic loci, two much less variable pentanucleotide repeats are also amplified and sized (PentaC and PentaD). The lengths of the amplicons covering PentaC and PentaD are only used to detect potential sample mix-ups or contamination, and are expected to be the same in normal and tumor samples.

Days Performed: Once a week.

In-Lab Turnaround Time: 10 days.

Specimen: Formalin-fixed, paraffin embedded tissue.

Collection Instructions:

Batched runs begin on Monday or first working day of each week. 

Provider must contact patient’s insurance about coverage for this molecular test and then counsel the patient on out-of-pocket costs.


For Unity and WI-MA patients, documented prior authorization will need to be present in Health Link or sent to laboratory before test will be collected and/or performed.


For all other managed care plans, referral must be placed in Health Link in order for testing on tissue or bone marrow specimens to be performed at UW Health; and patients should be referred to their primary care physician for collection of blood specimens.


For any other insurers, providers must check with insurer before ordering testing.

Stability Ambient:


Stability Refridgerated:


Stability Frozen:

Not acceptable

Sample Analyzed: Tissue

Specimen Processing:

Three slides each containing 5 microns (uM) of FFPE tissue should be sent. The second slide should be H&E stained with the normal and tumor circled. If necessary normal tissue can also be indicated on another slide from the same case. Please indicate percent tumor on Intra-Lab Send-Out Form.

If an add-on order is needed, please contact UWHC Surgical Pathology at (608)263-8443. A Surgical Pathology Tissue Examination Request form will need to be completed and faxed to (608)262-7174.


In order to ensure that molecular testing is conducted on a representative sample and a direct correlation of molecular results with morphologic findings is possible, a pathologist selects the specimen(s) and, whenever possible, identifies the suspicious or neoplastic cells submitted for molecular testing.

Outreach Specimen Processing:

Transport with a cold pack. Avoid excessive heat.

Specimen Transport:

Transport at room temperature.


No loci shows evidence of microsatellite instability (MSI-stable). A written interpretive report is provided by the laboratory.

Interpretation Type: Expected Results

Test Limitations:

Lack of evidence of microsatellite instability may be due to insufficient tissue or tumor present or to the presence of PCR inhibitors. The lower limit of detection for MSI DNA in a wild-type DNA background is approximately 10%.

Additional Information:

Inadequate specimen collection, processing and storage may invalidate test results. This test should not be used as the only criterion to form a clinical conclusion, instead, results should be correlated with other test results, patient symptoms and clinical presentation.


The performance characteristics of this test were validated by UWHC Clinical Laboratories. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test; however, FDA approval or clearance is currently not required for clinical use of this test. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions. The UWHC Clinical Laboratories is authorized under Clinical Laboratory Improvement Amendments (CLIA) to perform high-complexity testing.


A professional fee is associated with this test.