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Test ID: BAP1Z BAP1-Tumor Predisposition Syndrome, BAP1 Full Gene Analysis, Varies


Ordering Guidance


For a comprehensive hereditary renal cancer gene panel that includes testing for BAP1, consider RENCP / Hereditary Renal Cancer Panel, Varies.

 

Testing for the BAP1 gene as part of a customized panel is 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 this gene. For more information see FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Specimen Required


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 whole blood specimen in original tube. Do not aliquot.

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


Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file

-Informed Consent for Genetic Testing  (T576)

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

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

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

 

Useful For

Evaluating patients with a personal or family history suggestive of BAP1-tumor predisposition syndrome (BAP1-TPDS)

 

Establishing a diagnosis of BAP1-TPDS allowing for targeted cancer surveillance based on associated risks

 

Identifying genetic variants associated with increased risk for BAP1-TPDS, allowing for predictive testing and appropriate screening of at-risk family members

Genetics Test Information

This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in the BAP1 gene associated with BAP1-tumor predisposition syndrome (BAP1-TPDS). See Method Description for additional details.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for BAP1-TPDS.

Method Name

Sequence Capture and Targeted Next-Generation Sequencing followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing

Reporting Name

BAP1 Full Gene Analysis

Specimen Type

Varies

Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Clinical Information

Germline variants in the BAP1 gene are associated with BAP1-tumor predisposition syndrome (BAP1-TPDS), a rare autosomal dominant hereditary cancer syndrome.(1) BAP1-TPDS is characterized by increased risk to develop a variety of tumors, including BAP1-inactivated melanocytic tumor (also known as atypical Spitz tumor, or "BAPoma"), uveal and cutaneous melanoma, malignant mesothelioma, and renal cell carcinoma.(1) Many other tumor types, including basal cell carcinoma, hepatocellular carcinoma, cholangiocarcinoma, and meningioma, have also been associated with this syndrome.(1-6)

 

While the true penetrance of BAP1-TDPS is unknown due to both its rarity and ascertainment bias in the existing data, studies have shown up to 88% of individuals with an identified variant had a cancer diagnosis.(1,2)

 

Management and surveillance guidelines have been proposed by several multi-disciplinary expert groups.(1,5)

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(7) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Clinical Reference

1. Pilarski R, Carlo M, Cebulla C, Abdel-Rahman M: BAP1 tumor predisposition syndrome. In: Adam MP, Everman DB, Mirzaa GM, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2016. Updated March 24, 2022. Accessed November 8, 2022. Available at www.ncbi.nlm.nih.gov/books/NBK390611/

2. Walpole S, Pritchard AL, Cebulla CM, et al: Comprehensive study of the clinical phenotype of germline BAP1 variant-carrying families worldwide. J Natl Cancer Inst. 2018 Dec 1; 110(12):1328-1341. doi: 10.1093/jnci/djy171

3. Star P, Goodwin A, Kapoor R, et al: Germline BAP1-positive patients: the dilemmas of cancer surveillance and a proposed interdisciplinary consensus monitoring strategy. Eur J Cancer. 2018 Mar;92:48-53. doi: 10.1016/j.ejca.2017.12.022

4. Carbone M, Ferris LK, Baumann F, et al: BAP1 cancer syndrome: malignant mesothelioma, uveal and cutaneous melanoma, and MBAITs. J Transl Med. 2012 Aug 30;10:179. doi: 10.1186/1479-5876-10-179

5. Battaglia A: The importance of multidisciplinary approach in early detection of BAP1 tumor predisposition syndrome: Clinical management and risk assessment. Clin Med Insights Oncol. 2014 Apr 28;8:37-47. doi: 10.4137/CMO.S15239

6. Rai K, Pilarski R, Cebulla CM, Abdel-Rahman MH: Comprehensive review of BAP1 tumor predisposition syndrome with report of two new cases. Clin Genet. 2016 Mar;89(3):285-294. doi: 10.1111/cge.12630

7. 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 May;17(5):405-424. doi: 10.1038/gim.2015.30

Day(s) Performed

Varies

Report Available

21 to 28 days

Test Classification

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.

CPT Code Information

81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
BAP1Z BAP1 Full Gene Analysis 101381-2

 

Result ID Test Result Name Result LOINC Value
614623 Test Description 62364-5
614624 Specimen 31208-2
614625 Source 31208-2
614626 Result Summary 50397-9
614627 Result 82939-0
614628 Interpretation 69047-9
614629 Resources 99622-3
614630 Additional Information 48767-8
614631 Method 85069-3
614632 Genes Analyzed 48018-6
614633 Disclaimer 62364-5
614634 Released By 18771-6
Mayo Clinic Laboratories | Genetics and Genomics Additional Information:

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