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VistaSeq® Brain/CNS/PNS Cancer Panel

CPT: 81201; 81203; 81292; 81294; 81295; 81297; 81298; 81300; 81317; 81319; 81351; 81403(x2); 81404(x3); 81405(x2); 81406; 81408; 81479
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Synonyms

  • Familial Cancer testing
  • Hereditary Cancer testing
  • Inherited Cancer testing

Test Includes

ALK, APC, MEN1, MLH1, MSH2, MSH6, NBN, NF1, NF2, PHOX2B, PTCH1, RB1, SMARCB1, SUFU, TP53, and VHL.


Special Instructions

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


Expected Turnaround Time

23 - 28 days



Specimen Requirements


Specimen

Whole blood or saliva collected in an Oragene Dx collection kit


Volume

10 mL whole blood, 2 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


Collection

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


Storage Instructions

Room temperature


Stability Requirements

Temperature

Period

Room temperature

60 days

Refrigerated

60 days


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.


Test Details


Use

This assay is intended for patients with a family history consistent with an inherited cancer syndrome.


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 variations are assessed by microarray or multiple-ligation-probe amplification assay (MLPA) to detect gross deletions and duplications. 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 expanded to include promoter deletions for APC (1B and 1A). 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).


LOINC® Map

Order Code Order Code Name Order Loinc Result Code Result Code Name UofM Result LOINC
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481387 Specimen Type 31208-2
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481388 Preauthorization N/A
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481389 Result Summary 51968-6
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481390 Result and Interpretation 69548-6
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481391 Recommendations 47042-7
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481392 Additional Information 77202-0
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481393 Methodology and Limitations 49549-9
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481394 References 75608-0
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481395 Director Review 72486-4
481386 VistaSeq Brain/CNS/PNS Cancer 73977-1 481396 PDF 51969-4