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VistaSeq® Lynch Syndrome Panel

CPT 81292; 81294; 81295; 81297; 81298; 81300; 81319; 81403
Synonyms
  • Familial Cancer testing
  • Hereditary Cancer testing
  • Inherited Cancer testing

Test Details

Technology Used

Molecular, NGS

Turnaround Time

20 - 28 days

Use

This assay is intended for patients with a personal or family history consistent with Lynch syndrome.

Genes included: MLH1, MSH2, MSH6, PMS2, EPCAM

Special Instructions

A hereditary cancer clinical questionnaire should be submitted with all specimens. Contact CMBP genetic services at 800-345-4363 to coordinate testing.

Test Includes

MLH1, MSH2, MSH6, PMS2, and EPCAM.

Limitations

Sequencing cannot detect variants in regions not covered by this analysis, including noncoding or deep intronic variants and may not reliably detect changes in repetitive elements, such as microsatellite repeats. Sequencing may not detect mosaic variants, inversions, or other genomic rearrangements such as transposable element insertions. Sequence analysis may also be affected by allele drop-out due to the presence of a rare variant under a primer site or homopolymeric regions. The method does not allow any conclusion as to whether two heterozygous variants are present on the same or on different chromosome copies.

Copy number analyses are designed to detect single exon, multi-exon, and full gene deletions or duplications. These analyses may not detect certain genomic rearrangements, such as translocations (balanced or unbalanced), inversions, or some partial exon rearrangements. This assay cannot determine exact breakpoints of deletions or duplications detected.

The presence of pseudogenes can interfere with the ability to detect variants in certain genes. For example, deletion/duplication analysis of PMS2 exons 11-15, among others, is complicated by the highly homologous PMS2CL pseudogene. Deletions/duplications in PMS2CL have not been associated with Lynch syndrome, however this assay may not be able to determine if a deletion/duplication affects PMS2 or PMS2CL.

Each gene sequence is interpreted independently of all other gene sequences; however, variants in different genes may interact to cause or modify a typically monogenic disease phenotype.

In addition, the presence of an inherited cancer syndrome due to a different genetic cause cannot be ruled out. Any interpretation given should be clinically correlated with available information about presentation and the patient's relevant family history.

This test is not intended to detect somatic variants. Bone marrow transplantation may affect the outcome of these results. Please contact Labcorp at 1-800-345-GENE to discuss testing options.

This test was developed and its performance characteristics determined by Labcorp. It has not been cleared or approved by the Food and Drug Administration.

Methodology

The coding region and flanking splice sites are analyzed by NGS (+/-10bp) and deletion/duplication analysis. Exon-level deletions/duplications are assessed by aCGH or by MLPA. Analysis is limited to deletion/duplication testing for EPCAM. Clinically significant findings are confirmed by Sanger sequencing or qPCR. Results are reported using ACMG guidelines and nomenclature recommended by the Human Genome Variation Society (HGVS).

Specimen Requirements

Information on collection, storage, and volume

Specimen

Whole blood or saliva collected in an Oragene Dx collection kit

Volume

10 mL whole blood, 2.0 mL saliva

Minimum Volume

7 mL whole blood, 0.5 mL saliva

Container

Lavender-top (EDTA) tube or yellow-top (ACD) tube or Oragene Dx 500 saliva collection kit

Storage Instructions

Room temperature or refrigerated

Causes for Rejection

Frozen specimen; leaking tube; clotted specimen; grossly or hemolyzed specimen; quantity not sufficient for analysis; incorrect anticoagulant; saliva collection in an incorrect container. Do not eat, drink, smoke, or chew gum 30 minutes prior to saliva sample collection. See Oragene Dx 500 saliva kit for detailed instructions.

Collection

Blood is collected by routine phlebotomy. Saliva is collected by spitting into the provided container until it reaches the fill line.