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STAT PMS2 Gene Test
STAT PMS2 Gene Test
Test code:
D5114F
STAT PMS2 Gene Test
This test analyzes the PMS2 gene, which is associated with Lynch syndrome.
| Test Code | D5114F |
|---|---|
| Test Summary |
This test analyzes the PMS2 gene, which is associated with Lynch syndrome. |
| Turn Around Time | 7 - 10 days |
| Acceptable Sample Types | DNA, Isolated , Dried Blood Spots , Saliva , Whole Blood (EDTA) |
| Acceptable Billing Types | Institutional Billing , Self (patient) Payment |
| NY Approved | No |
| CPT Codes** | 81317(x1), 81319(x1) |
| Self (patient) Price | $1,500.00 |
|---|---|
| Institutional Price | $1,750.00 |
*TAT starts after the sample and all required sample information is received at the processing laboratory.
**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.
This testing service has not been cleared or approved by the U.S. Food and Drug Administration. Testing services may not be licensed in accordance with the laws in all countries. The availability of specific test offerings is dependent upon laboratory location.
**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.
This testing service has not been cleared or approved by the U.S. Food and Drug Administration. Testing services may not be licensed in accordance with the laws in all countries. The availability of specific test offerings is dependent upon laboratory location.
Test code:
D5114F
Resources
Test information
Test description
This panel includes both sequencing and deletion/duplication (CNV) analysis of the coding regions of the PMS2 gene. PMS2 gene sequencing is greatly complicated by numerous unprocessed PMS2 pseudogenes. For regions that might have pseudogene interference, long-range polymerase chain reaction (LR-PCR) followed by nested PCR and Sanger sequencing is used to accurately detect variants in the PMS2 gene. For regions without pseudogenes, PCR is used directly to amplify targeted regions followed by Sanger sequencing. Deletion/duplication (CNV) analysis is completed via multiplex ligation-dependent probe amplification (MLPA). All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.
Condition description
Pathogenic mutations in the PMS2 gene are associated with Lynch syndrome, or hereditary nonpolyposis colorectal cancer, which is a hereditary cancer syndrome characterized by an increased risk of colorectal cancer, as well as other types of cancer, and is caused by mutations in genes involved in DNA mismatch repair. Individuals with Lynch syndrome have a significantly increased risk of developing colorectal cancer at an earlier age compared to the general population. Colorectal cancer may occur in the 20s or 30s, although the average age of onset is around 45 years. Lynch syndrome is associated with an increased risk of other cancers, including endometrial, ovarian, stomach, small intestine, urinary tract, pancreatic, and bile duct. Individuals with Lynch syndrome is typically have a strong family history of cancer, particularly colorectal and endometrial cancer, across multiple generations. Individuals with Lynch syndrome require regular cancer surveillance and management to detect cancers at an early, more treatable stage.
Genes
PMS2
Test methods and limitations
PMS2 long-range PCR was performed to capture the genomic sequences for the real PMS2 gene from this individual’s genomic DNA to prevent the pseudogene from being co-amplified. Next-generation sequencing (NGS) was performed on an Illumina system with 100 base pair paired-end reads. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. Low coverage regions, if any, are limited to ~1% or less of the nucleotides in the test unless a pathogenic variant explaining the phenotype is discovered. A list of these regions is available upon request. Alignment to the human reference genome (hg19) is performed and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indels and Single nucleotide variants (SNVs) are confirmed by Sanger sequence analysis before reporting at the director's discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions or long repetitive regions. Copy number variation (CNV) analysis was assessed using MLPA. This analysis cannot determine the location or orientation of a duplication. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director.
Detailed sample requirements
DNA, Isolated
| Collection |
Required DNA Quantity by Test Type*:
|
|---|---|
| Sample Condition |
* Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met. |
| Shipping |
Ship overnight at ambient temperature. |
| SPECIAL SAMPLE INSTRUCTIONS |
|
Whole Blood (EDTA) (Preferred Sample)
| Collection Container(s) |
EDTA (purple top) |
|---|---|
| Collection |
Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation. |
| Sample Condition |
Store at ambient temperature. Do not refrigerate or freeze. |
| Shipping |
Ship overnight at ambient temperature ensuring receipt within 5-days of collection. |
| SPECIAL SAMPLE INSTRUCTIONS |
Clotted or hemolyzed samples are not accepted. |
Saliva
| Collection Container(s) |
Oragene™ Saliva Collection Kit or ORAcollect-Dx kit |
|---|---|
| Collection |
Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer's instructions. |
| Sample Condition |
Store at ambient temperature. Do not refrigerate or freeze. |
| Shipping |
Ship overnight at ambient temperature. |
| SPECIAL SAMPLE INSTRUCTIONS |
Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information. |
Dried Blood Spots
| Collection Container(s) |
Dried blood spot card |
|---|---|
| Collection |
Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours.
|
| Sample Condition |
Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer. |
| Shipping |
Follow kit instructions. Double bag and ship overnight at ambient temperature. |
Resources
How To Order
Step 1
Choose Your Test
Select the correct test for your patient, and download and fill out the Clinical Genomics test requisition form.
Step 2
Collect Sample
Obtain a sample for testing from the patient using one of the provided Revvity Omics test packs.
Step 3
Send Samples
Send samples and all required forms back to Revvity for processing using pre-paid shipping label.
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