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Lynch Syndrome via MLPA of PMS2

Summary and Pricing

Test Method

Multiplex Ligation-Dependent Probe Amplification Assay
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
6062 PMS2 81319 81319 $540 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
6062PMS281319 81319 $540 Order Options and Pricing

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Yuan Xue, PhD

Clinical Features and Genetics

Clinical Features

Lynch syndrome, also known as hereditary nonpolyposis colorectal cancer (HNPCC), is an autosomal dominant inherited cancer syndrome associated with germline pathogenic variants in the DNA mismatch repair (MMR) genes MLH1MSH2MSH6, and PMS2 as well as the EPCAM gene (Peltomäki and Vasen. 2004. PubMed ID: 15528792; Idos and Valle. 2021. PubMed ID: 20301390). The prevalence of Lynch syndrome is estimated at 1 per 279 individuals but varies by gene (Win et al. 2017. PubMed ID: 27799157). The prevalence of PMS2-associated Lynch syndrome is estimated at 1 per 714 individuals (Win et al. 2017. PubMed ID: 27799157). Individuals with a monoallelic (heterozygous) PMS2 pathogenic variant have higher lifetime risks of colorectal, endometrial, ovarian, prostate, and other types of cancer compared to individuals in the general population (Idos and Valle. 2021. PubMed ID: 20301390).

Testing asymptomatic and symptomatic individuals at increased risk of a hereditary cancer syndrome, such as Lynch syndrome, may inform genetic counseling, screening, prevention strategies, and treatment (Weitzel et al. 2011. PubMed ID: 21858794; ACOG. 2019. PubMed ID: 31764758). It also may be considered if a positive finding will impact medical management for the individual or their at-risk family members.

Of note, the PMS2 gene is also associated with a rare autosomal recessive cancer-related syndrome called constitutional mismatch repair deficiency syndrome (CMMR-D). CMMR-D is characterized by childhood malignancies, mainly hematological or neurological, and neurofibromatosis-like café au lait spots. Approximately 50% of individuals with CMMR-D have biallelic PMS2 pathogenic variants (Wimmer and Etzler. 2008. PubMed ID: 18709565). For individuals harboring a monoallelic PMS2 pathogenic variant, there may be a risk of CMMR-D in offspring if an individual’s partner is also a carrier of a PMS2 pathogenic variant.

Genetics

PMS2 is an MMR gene involved in DNA repair and maintenance of genomic integrity (Blount and Prakash. 2018. PubMed ID: 29286535). Most pathogenic variants are inherited from one or both parents.

DNA analysis of the PMS2 gene is complicated due to the presence of several pseudogenes. One particular pseudogene, PMS2CL, has high sequence similarity to PMS2 exons 11 through 15 (Blount and Prakash. 2018. PubMed ID: 29286535). However, deletion and duplication analysis via multiplex ligation-dependent probe amplification (MLPA) is able to able to distinguish between the native PMS2 gene and its pseudogenes, including PMS2CL.

Clinical Sensitivity - MLPA

Approximately 5% to 25% of Lynch Syndrome is attributed to pathogenic variants in PMS2 (Idos and Valle. 2021. PubMed ID: 20301390). Of these pathogenic variants, 45% to 80% are single nucleotide substitutions or small insertions and deletion detected via sequence analysis, and 20% to 55% are copy number variants detected via gene-targeted deletions and duplication analysis (Idos and Valle. 2021. PubMed ID: 20301390).

Testing Strategy

Multiplex ligation-dependent probe amplification (MLPA) enables the detection of deletion and duplications of single and multiple exons within a given gene (Eijk-Van Os and Schouten. 2011. PubMed ID: 20938835). It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides of approximately 60 nucleotides in length are amplified using PCR and thus are specific for the sequence of interest. A stuffer sequence attached to the probe ensures a particular length for deciphering the probe target. Therefore, MLPA enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. For additional information, please see www.mlpa.com.

Indications for Test

Candidates for this test are patients with Lynch syndrome or CMMR-D, and relatives of patients with a verified PMS2 variant. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PMS2. This test is specifically designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.

Gene

Official Gene Symbol OMIM ID
PMS2 600259
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Cancer Panel
Colorectal Cancer Panel
Common Hereditary Cancer Screening Panel
Lynch Syndrome Panel
Lynch Syndrome via the PMS2 Gene

Citations

  • American College of Obstetricians and Gynecologists. 2019. PubMed ID: 31764758
  • Blount and Prakash. 2018. PubMed ID: 29286535
  • Eijk-Van Os and Schouten. 2011. PubMed ID: 20938835
  • Idos and Valle. 2021. PubMed ID: 20301390
  • Peltomäki and Vasen. 2004. PubMed ID: 15528792
  • Weitzel et al. 2011. PubMed ID: 21858794
  • Wimmer and Etzler. 2008. PubMed ID: 18709565
  • Win et al. 2017. PubMed ID: 27799157

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

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View Ordering Instructions

1) Select Test Method (Platform)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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