VistaSeq℠ Hereditary Cancer Panel Without BRCA

CPT: 81201; 81203; 81292; 81294; 81295; 81297; 81298; 81300; 81317; 81319; 81321; 81323; 81403; 81404(x2); 81405(x3); 81406(x4); 81408; 81479
Updated on 11/17/2018
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Test Details

Test Includes

The following genes are assessed: APC, ATM, BARD1, BMPR1A, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, FAM175A, MLH1, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PRKAR1A, PTEN, RAD51C, RAD51D, SMAD4, STK11, TP53.

Use

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

The VistaSeq℠ Hereditary Cancer Panel Without BRCA provides an assessment of inherited genetic mutations within a panel of 25 genes known to be associated with hereditary cancer syndromes. The test is intended for individuals who have already had a BRCA1 and BRCA2 gene assessment, but for whom results of that testing were negative and/or personal or family history warrant assessment of additional genes.

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 US Food and Drug Administration (FDA).

Each gene sequence is interpreted independently of all other gene sequences; however, variants in different genes may sometimes interact to cause or modify a typically monogenic disease phenotype. It cannot be excluded that pathogenic variants were missed due to limitations inherent in the methodologies used here. In addition, the presence of an inherited cancer syndrome due to a different genetic cause can also not be ruled out. Any interpretation given here should be clinically correlated with available information about presentation and relevant family history of the patient.

This test was developed, and its performance characteristics determined, by LabCorp. It has not been cleared or approved by the US Food and Drug Administration (FDA).

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 US Food and Drug Administration (FDA).

Methodology

The entire coding region of a panel of genes related to hereditary cancer is examined by next generation sequencing analysis. Additionally, portions of the flanking noncoding regions are also examined. Comprehensive deletion/ duplication testing is performed using microarray CGH for and / or by multiplex ligation-dependent probe amplification (MLPA). Genes tested in this panel include APC, ATM, BARD1, BMPR1A, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, FAM175A, MLH1, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PRKAR1A, PTEN, RAD51C, RAD51D, SMAD4, STK11, and TP53. 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).

Next generation sequencing, array-based comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) platforms. The entire coding regions, as well as all flanking noncoding regions, of 25 cancer genes known to be involved in the development and progression of cancers are analyzed by next generation sequencing. Flanking regions for all genes include +/– 20 bp and +/– 10 bp. Copy number variations are assessed by aCGH or MLPA to detect deletions and duplications. BRCA1 and BRCA2 genes are not included in this test.

The entire coding region of a panel of genes related to hereditary cancer is examined by next generation sequencing analysis. Additionally, portions of the flanking noncoding regions are also examined. Comprehensive deletion/ duplication testing is performed using microarray CGH for and / or by multiplex ligation-dependent probe amplification (MLPA). Genes tested in this panel include APC, ATM, BARD1, BMPR1A, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, FAM175A, MLH1, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PRKAR1A, PTEN, RAD51C, RAD51D, SMAD4, STK11, and TP53. 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

Specimen

Whole blood

Volume

10 mL

Minimum Volume

7 mL

Container

Lavender-top (EDTA) tube or yellow-top (ACD) tube

Collection

Blood is collected by routine phlebotomy.

Storage Instructions

Room temperature

Causes for Rejection

Frozen specimen; leaking tube; clotted specimen; grossly hemolyzed specimen; incorrect anticoagulant

Clinical Information

Special Instructions

Test orders must include an attestation that the provider has the patient's informed consent for genetic testing. See sample physician office consent form (Informed Consent for VistaSeq℠) in Related Documents. A Hereditary Cancer Clinical Questionnaire also should be submitted with specimens. Contact CMBP genetics services at 800-345-4363 to coördinate testing.

References

Daly MB, Axilbund JE, Buys S, et al. Clinical practice guidelines in oncology. Genetic/familial high-risk assessment: Breast and ovarian. J Natl Compr Canc Netw. 2010 May; 8(5):562-594. 20495085
LaDuca H, Stuenkel AJ, Dolinsky JS, et al. Utilization of multigene panels in hereditary cancer predisposition testing: Analysis of more than 2,000 patients. Genet Med. 2014 Nov; 16(11):830-837. 24763289
Rehm HL, Bale SJ, Bayrak-Toydemir P, et al. Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013 Sep; 15(9):733-747. 23887774
Tung N, Battelli C, Allen B, et al. Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Cancer. 2015 Jan 1; 121(1):25-33. 25186627

LOINC® Map

Order Code Order Code Name Order Loinc Result Code Result Code Name UofM Result LOINC
481240 VistaSeq Hered Cancer w/o BRCA 481239 Specimen Type 31208-2
481240 VistaSeq Hered Cancer w/o BRCA 481234 Preauthorization N/A
481240 VistaSeq Hered Cancer w/o BRCA 481246 Result Summary 51968-6
481240 VistaSeq Hered Cancer w/o BRCA 481247 Result and Interpretation 69548-6
481240 VistaSeq Hered Cancer w/o BRCA 481248 Recommendations 47042-7
481240 VistaSeq Hered Cancer w/o BRCA 481249 Additional Information 77202-0
481240 VistaSeq Hered Cancer w/o BRCA 481250 Methodology and Limitations 49549-9
481240 VistaSeq Hered Cancer w/o BRCA 481251 References 75608-0
481240 VistaSeq Hered Cancer w/o BRCA 481252 Director Review 72486-4
481240 VistaSeq Hered Cancer w/o BRCA 481253 PDF 51969-4

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