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STAT PMS2 Gene Test

Test code: D5114F

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Test code: D5114F

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STAT PMS2 Gene Test

This test analyzes the PMS2 gene, which is associated with Lynch syndrome.

View test information

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	$900.00
Institutional Price	$1,200.00

*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.

Test code: D5114F

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Resources

Clinical Genomics Test Requisition Form

Order Tests Test Inquiry

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

Test Details Page
Collection	Required DNA Quantity by Test Type: Next Generation Sequencing (NGS):* Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA. Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested). Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.
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	Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results. Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor before submitting a DNA sample from any non-CLIA-certified laboratory. Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.

Whole Blood (EDTA) (Preferred Sample)

Test Details Page
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

Test Details Page
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

Test Details Page
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. NBS: Please contact Revvity Omics to request the StepOne^® kit. Gene Sequencing: Please contact Revvity Omics to request the DBS collection kit. For pre-punched DBS: The required minimum is 6 punches
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

Clinical Genomics Test Requisition Form

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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Revvity Sites Globally

STAT PMS2 Gene Test

STAT PMS2 Gene Test

STAT PMS2 Gene Test

About this test

Specifications

Price

Test information

Test description

Condition description

Genes

Test methods and limitations

Detailed sample requirements

DNA, Isolated

Whole Blood (EDTA) (Preferred Sample)

Saliva

Dried Blood Spots

Resources

How To Order

Choose Your Test

Collect Sample

Send Samples

How can we help you?

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STAT PMS2 Gene Test

STAT PMS2 Gene Test

STAT PMS2 Gene Test

About this test

Specifications

Price

Test information

Test description

Condition description

Genes

Test methods and limitations

Detailed sample requirements

DNA, Isolated

Whole Blood (EDTA) (Preferred Sample)

Saliva

Dried Blood Spots

Resources

How To Order

Choose Your Test

Collect Sample

Send Samples

1. Build Your Custom Panel

2. Complete and print the test requisition

3. Collect and Send Patient Sample

How can we help you?