Test Code: 8570

BRAF-related Disorders: BRAF Gene Sequencing
Test Code: 8570
Turnaround time: 5 weeks

CONDITION DESCRIPTION

Germline mutations in the BRAF gene have been reported to be associated with cardiofaciocutaneous (CFC) syndrome. Somatic mutations in BRAF have also been reported at a high frequency in numerous cancers.

CFC Syndrome
Cardiofaciocutaneous (CFC) syndrome is characterized by features in three primary systems: cardiac, craniofacial, and ectodermal; however, other systems may be involved as well. Cardiac abnormalities can include pulmonic stenosis and other valve dysplasias, septal defects, hypertrophic cardiomyopathy, and rhythm disturbances. Individuals with CFC syndrome have a distinctive craniofacial appearance. Ectodermal features include skin findings, such as xerosis, hyperkeratosis, ichthyosis, keratosis pilaris, ulerythema oophorogenes, eczema, pigmented moles, palmoplantar hyperkeratosis; hair findings such as sparse, curly, fine or thick, woolly, or brittle hair, and possible absent eyelashes and eyebrows; and the nails may be dystrophic or fast growing. Cognitive delay (ranging from mild to severe) is seen in all affected individuals. Neoplasias have been reported in some individuals with CFC.

There are four genes known to be associated with CFC. Mutations in the BRAF gene account for ~75% of cases, MAP2K1 and MAP2K2 account for ~25% of cases, and KRAS accounts for <2% of cases. CFC syndrome is inherited in an autosomal dominant manner; however, most cases of CFC syndrome arise de novo.

Cancer
Somatic mutations in BRAF have been reported at a high frequency in numerous cancers including melanoma, thyroid, colorectal, and ovarian. One mutation, p.V600E, which results in increased kinase activity, accounts for more than 90% of BRAF mutations identified in human cancer. The presence of the p.V600E BRAF mutation in microsatellite instability high (MSI-H) colorectal cancers provides evidence that the cancer is sporadic and not caused by Lynch syndrome.

Testing for the p.V600E BRAF mutation can be ordered by marking “Other test” and then test code 6875 next to it on the test requisition. Do this by writing “p.V600E BRAF, 6875.”
Please note that this test is for the BRAF (7q35) gene only.

References:

  • Bettstetter, M. et al. Distinction of hereditary nonpolyposis colorectal cancer and sporadic microsatellite-unstable colorectal cancer through quantification of MLH1 methylation by real-time PCR. Clin Cancer Res. 2007; 13:3221-3228.
  • Domingo, E. et al. BRAF screening as a low-cost effective strategy for simplifying HNPCC genetic testing. J Med Genet. 2004: 41:664-668.

GENES
BRAF

INDICATIONS
This test is indicated for:

  • Confirmation of a clinical diagnosis of a CFC syndrome

METHODOLOGY

PCR amplification of 18 exons of the BRAF gene is performed on the patient’s genomic DNA. Direct sequencing of amplification products is performed in both forward and reverse directions, using automated fluorescence dideoxy sequencing methods. The patient’s gene sequences are then compared to a normal reference sequence. Sequence variations are classified as mutations, benign variants unrelated to disease, or variations of unknown clinical significance. Variants of unknown clinical significance may require further studies of the patient and/or family members. This assay does not interrogate the promoter region, deep intronic regions, other regulatory elements, or the remaining 11 exons, and does not detect large deletions.

DETECTION

Clinical Sensitivity: BRAF mutations have been implicated in 75-80% of cases of CFC syndrome. Mutations in the promoter region and some mutations in the introns and other regulatory elements cannot be detected by this analysis. Large deletions will not be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient’s biochemical phenotype.

Analytical Sensitivity: ~99%

SPECIMEN REQUIREMENTS

Submit only 1 of the following specimen types
* Preferred specimen type: Whole Blood

Type: Whole Blood
Specimen Requirements:
In EDTA (purple top) or ACD (yellow top) tube: Infants (2 years): 3-5 ml
Older Children & Adults: 5-10 ml

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample within 5 days of collection at room temperature with overnight delivery.

Type: Saliva
Specimen Requirements:
OrageneTM Saliva Collection kit (available through CEN4GEN) used according to manufacturer instructions.

Specimen Collection and Shipping: Store sample at room temperature. Ship sample within 5 days of collection at room temperature with overnight delivery.

RELATED TESTS

  • Deletion/duplication analysis is available if sequencing is negative.
  • Sequence and deletion/duplication analysis of the KRAS, SOS1, RAF1, MAP2K1, MAP2K2 and PTPN11 genes are available.
  • Custom diagnostic mutation analysis (test code: 6875) is available to family members if mutations are identified by targeted mutation testing or sequencing analysis.