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Microsatellite Instability by PCR

Item Value
Approval req'd? No
Available Stat? No
Utilization Guidelines Criteria for HNPCC testing (revised Bethesda guidelines):

1. Colorectal cancer diagnosed in a patient who is less than 50 years of age.

2. Presence of synchronous, metachronous colorectal, or other HNPCC-associated tumors, regardless of age. HNPCC-associated tumors include colorectal, endometrial, stomach, ovarian, pancreas, ureter and renal pelvis, biliary tract, and brain (usually glioblastoma as seen in Turcot syndrome) tumors; sebaceous gland adenomas and keratoacanthomas in Muir-Torre syndrome; and small bowel carcinoma.

3. Colorectal cancer with the MSI-H histology diagnosed in a patient who is less than 60 years of age. Note that inclusion of the age criteria is controversial.

4. Colorectal cancer in a patient with one or more first-degree relatives with an HNPCC-related tumor, with one of the cancers being diagnosed under age 50 years.

5. Colorectal cancer in a patient with two or more first- or second-degree relatives with HNPCC-related tumors, regardless of age.

UCSF Clinical criteria for HNPCC testing in gynecologic tumors:

Nearly half of women with HNPCC will present with a gynecologic tumor, rather than a colon cancer.

1. Endometrioid histology at any GYN location in a patient under 50 in a definitive surgical procedure (i.e., not just biopsy, wait for primary surgery).

2. Any adenocarcinoma at any GYN location in a patient with colon cancer.

3. Clinician suspicion for Lynch syndrome.

Note: BRAF V600E Mutation testing may be performed on samples that are MSI-High and show loss of MLH1 by immunohistochemistry to distinguish the sporadic MSI-high cases (BRAF mutation positive) vs. the MSI-high cases associated with Lynch syndrome (BRAF mutation negative
Test code
Performed by Applied Genomics Clinical Laboratory
In House Availability Test performed once a week, with DNA extraction set up on Mondays and Wednesdays, test run on Tuesday or Wednesday, day shift only
Method Multiplex PCR with analysis by capillary electrophoresis
Collection Instructions Testing should be ordered only on surgical excision samples. Biopsy material is not appropriate. Blocks selected for MSI PCR testing must contain both tumor and normal tissue. If only tumor is present on the block, select an additional block with normal tissue

Areas of tumor must contain at least 50% tumor cells. The lab can remove adjacent non-tumor tissue, so the entire slide does not need 50% tumor cells, just the area with tumor. Contact the laboratory (415-514-1035, AGCLab@ucsf.edu) if the specimen suitability is uncertain. Label slides with pathology case number and block identification.

Complete an Applied Genomics Laboratory requisition and submit it with samples.

Click here for requisition form
Container type
Sample type Formalin-fixed, paraffin-embedded tissue. Tissue block or unstained slides. If sending unstained slides, we require five (5) 10-micron tissue sections on uncharged glass slides. One adjacent H&E stained slide should be included.
UCSF Rejection Criteria All required slides not included. Insufficient tumor or normal tissue present on slide as determined by pathologist. Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Normal range
Synonyms MSI; HNPCC testing; Hereditary non-polyposis Colon cancer; Hereditary non-polyposis Colorectal cancer
Stability Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Turn around times 7-10 days
Additional information An interpretation of this test by a laboratory physician will automatically be performed and billed for separately.

This test is typically run in conjunction with immunohistochemical staining for mismatch repair proteins, performed by the UCSF Pathology Laboratory. Microsatellite Instability by PCR may also be ordered as a separate test.

Microsatellite Instability by PCR is designed to aid in the identification of patients who harbor germline mutations in mismatch repair (MMR) proteins that are associated with HNPCC. It is important to note that defective MMR resulting in MSI can also arise spontaneously in a tumor (i.e., without inheritance of a mutant MMR gene), and therefore the presence of MSI is not diagnostic for Lynch syndrome/Hereditary Non-Polyposis Colorectal Cancer (HNPCC).

Results from this test should be correlated with the patient's clinical presentation, family history and any findings from immunohistochemical staining for mismatch repair proteins in the tumor. Genetic counseling may be recommended for some cases.

BRAF V600E Mutation testing may be performed on colorectal samples that are MSI-High and show loss of MLH1 by immunohistochemistry to distinguish the sporadic MSI-high cases (BRAF mutation positive) from the MSI-high cases associated with Lynch syndrome (BRAF mutation negative). Note that not all MSI-H colorectal cancers that lack BRAF mutation are due to Lynch syndrome.

The test was validated by the UCSF Applied Genomics Clinical Laboratory to confirm performance characteristics, in compliance with current guidelines for clinical implementation.

The Microsatellite Instability by PCR assay utilizes a multiplex PCR reaction which amplifies five mononucleotide repeat markers (BAT-25, BAT-26, NR-21, NR-24 and MONO-27). A histologic section of formalin-fixed, paraffin-embedded tissue is examined by a pathologist to identify areas of tumor and normal tissue. DNA is extracted separately from tumor and normal areas on adjacent unstained slides and amplified in the multiplex PCR reaction. Fluorescently labeled PCR products are identified and sized by capillary electrophoresis. Markers are scored for stability or instability by comparison of marker allele sizes from tumor and normal samples. The presence of a marker allele size in the tumor sample that is not present in the normal sample is indicative of instability for that marker. The number of unstable markers is used to determine the presence or absence of instability.
CPT coding 81301
LDT or Mod FDA? Yes
Last Updated 2/28/2014 2:52:51 PM
Entry Number 1163
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