Test Id : XCP

Customization of this panel and single gene analysis for any gene present on this panel are available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.

Targeted testing for familial variants (also called site-specific or known mutations testing) is available for the genes on this panel. For more information see FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.

Testing minors for adult-onset predisposition syndromes is discouraged by the American Academy of Pediatrics, the American College of Medical Genetics and Genomics, and the National Society of Genetic Counselors.

Specimen preferred to arrive within 96 hours of collection.

Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated

• Molecular Genetics: Inherited Cancer Syndromes Patient Information
• Informed Consent for Genetic Testing
• Informed Consent for Genetic Testing (Spanish)
• Targeted Genes and Methodology Details for Hereditary Expanded Cancer Panel

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing (Spanish) (T826)

2. Molecular Genetics: Inherited Cancer Syndromes Patient Information (T519)

3. If not ordering electronically, complete, print, and send a Oncology Test Request (T729) with the specimen.

1 mL

Evaluating hereditary cancer in patients with a personal or family history suggestive of a hereditary cancer syndrome

Establishing a diagnosis of a hereditary cancer syndrome allowing for targeted cancer surveillance based on associated risks

Identifying genetic variants associated with increased risk for cancer, allowing for predictive testing and appropriate screening of at-risk family members

Therapeutic eligibility with poly adenosine diphosphate-ribose polymerase (PARP) inhibitors based on certain gene alterations (eg, BRCA1, BRCA2) in selected tumor types

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 87 genes associated with a variety of hereditary cancer syndromes: AIP, ALK, APC (including promoters 1A and 1B), ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, BUB1B, CDC73, CDH1, CDK4, CDKN1B, CDKN2A, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, ELP1, EPCAM (copy number variants only), EXT1, EXT2, FANCA, FH, FLCN, GPC3, GREM1 (upstream enhancer region duplication only), HOXB13, KIT, LZTR1, MAX, MC1R, MEN1, MET, MITF (c.952G>A p.E318K variant only), MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN (including promoter), RAD51B, RAD51C, RAD51D, RB1, RECQL4, REST, RET, RNF43, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TMEM127, TP53, TRIP13, TSC1, TSC2, VHL, WRN, WT1. See Method Description and Targeted Genes and Methodology Details for Hereditary Expanded Cancer Panel for additional details.

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for a variety of hereditary cancer syndromes.

Hereditary cancer syndromes explain about 5% to 10% of cancer cases.(1,2) Determining if there is a genetic risk factor contributing to cancer in an individual or family can be useful for tailoring surveillance plans, consideration of prophylactic risk reducing interventions, targeted cancer treatments, and determining risk for family members.(3)

This panel evaluates 87 genes associated with an increased risk for the following cancers: breast, colon, gastric, ovarian, pancreatic, prostate, renal, skin, thyroid, and endometrial cancers, as well as paragangliomas, pheochromocytomas, and Wilms tumor.

The risk for developing cancer associated with these syndromes varies. Several of the of the genes on this panel have established cancer risk and National Comprehensive Cancer Network (NCCN) or expert group guidelines and recommendations for management.(4-9)

Indications for testing include but are not limited to:

-Individuals with multiple primary cancers

-Individuals with cancer diagnosed at young age

-Individuals with a family history of multiple relatives with cancer

-Individuals whose family history of cancer may seem to overlap with more than one hereditary cancer syndrome

An interpretive report will be provided.

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(10) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Clinical Correlations:

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.

To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact the Mayo Clinic Laboratories genetic counselors at 800-533-1710.

Technical Limitations:

Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.

This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.

Deletion/Duplication Analysis:

This analysis targets single and multi-exon deletions/duplications; however, in some instances, single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.

This test is not designed to detect low levels of mosaicism or to differentiate between somatic and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.

Genes may be added or removed based on updated clinical relevance. For the most up to date list of genes included in this test, detailed information regarding gene specific performance, and technical limitations, see Method Description or Targeted Genes and Methodology Details for Hereditary Expanded Cancer Panel or contact a laboratory genetic counselor.

If the patient has had an allogeneic hematopoietic stem cell transplant or a recent blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received a bone marrow transplant.

Reclassification of Variants Policy:

Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages healthcare providers to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time.

Variant Evaluation:

Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline.(10) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. Variants classified as benign or likely benign are not reported.

Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.

1. Howlader N, Noone AM, Krapcho M, et al. SEER Cancer Statistics Review. 1975-2018. National Cancer Institute. Updated April 2021. Accessed November 9, 2022. Available at: https://seer.cancer.gov/csr/1975_2018/

2. Nagy R, Sweet K, Eng C. Highly penetrant hereditary cancer syndromes. Oncogene. 2004;23(38):6445-6470

3. Samadder NJ, Rigert-Johnson D, Boardman L, et al. Comparison of universal genetic testing vs guideline-directed targeted testing or patients with hereditary cancer syndrome. JAMA Oncol. 2021 Feb 1;7(2):230-237

4. Daly MB, Pal T, Berry MP, et al. Genetic/familial high-risk assessment: Breast, ovarian, and pancreatic, Version 2.2021, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw. 2021;19(1):77-102

5. Gupta S, Provenzale D, Llor X, et al. NCCN Guidelines Insights: Genetic/familial high-risk assessment: colorectal, version 2.2019. J Natl Compr Canc Netw. 2019;17(9):1032-1041

6. Coit DG, Thompson JA, Albertini MR, et al. Cutaneous melanoma, Version 2.2019, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw. 2019;17(4):367-402

7. Haddad RI, Nasr C, Bischoff L, et al. NCCN Guidelines Insights: Thyroid carcinoma, Version 2.2018. J Natl Compr Canc Netw. 2018;16(12):1429-1440

8. Saslow D, Boetes C, Burke W, et al. American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CA Cancer J Clin. 2007;57(2):75-89

9. Smith RA, Andrews KS, Brooks D, et al. Cancer screening in the United States, 2019: A review of current American Cancer Society guidelines and current issues in cancer screening. CA Cancer J Clin. 2019;69(3):184-210

10. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-424

Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions-insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS, multiplex ligation-dependent probe amplification (MLPA), and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. PCR and gel electrophoresis is performed to test for the presence of the 10 megabase inversion of coding exons 1-7 of the MSH2 gene.

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. For details regarding the targeted genes analyzed and specific gene regions not routinely covered see Targeted Genes and Methodology Details for Hereditary Expanded Cancer Panel.(Unpublished Mayo method)

Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.

Genes analyzed: AIP, ALK, APC (including promoters 1A & 1B), ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, BUB1B, CDC73, CDH1, CDK4, CDKN1B, CDKN2A, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, ELP1, EPCAM (copy number variants only), EXT1, EXT2, FANCA, FH, FLCN, GPC3, GREM1 (upstream enhancer region duplication only), HOXB13, KIT, LZTR1, MAX, MC1R, MEN1, MET, MITF (c.952G>A p.E318K variant only), MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN (including promoter), RAD51B, RAD51C, RAD51D, RB1, RECQL4, REST, RET, RNF43, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TMEM127, TP53, TRIP13, TSC1, TSC2, VHL, WRN, and WT1

Varies

• Authorized users can sign in to Test Prices for detailed fee information.
• Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
• Prospective clients should contact their account representative. For assistance, contact Customer Service.

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.

81162

81201

81292

81295

81298

81307

81317

81319

81321

81351

81403

81404 x4

81405 x6

81406 x7

81407

81408 x2

81479

81479 (if appropriate for government payers)