Test Code NF1Z Neurofibromatosis Type 1, NF1, Full Gene Analysis, Varies

Ordering Guidance

For a comprehensive hereditary cancer panel that includes the NF1 gene, consider ordering 1 of the following tests:

-BRGYP / Hereditary Breast/Gynecologic Cancer Panel, Varies

-ENDCP / Hereditary Endocrine Cancer Panel, Varies

-HPGLP / Hereditary Paraganglioma/Pheochromocytoma Panel, Varies

Testing for NF1 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. 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 Sheet (T519)

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

Secondary ID

614585

Useful For

Evaluating patients with a personal or family history suggestive of neurofibromatosis type 1 (NF1)

Establishing a diagnosis of a NF1 allowing for targeted cancer surveillance based on associated risks

Identifying genetic variants associated with increased risk for NF1 allowing for predictive testing of at-risk family members

Special Instructions

Method Name

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

Reporting Name

NF1 Full Gene Analysis

Specimen Type

Varies

Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type	Temperature	Time	Special Container
Varies	Varies

Reject Due To

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Clinical Information

Germline variants in the NF1 gene are associated with neurofibromatosis type 1 (NF1), an autosomal dominant hereditary tumor syndrome.(1) NF1 is characterized by many manifestations beginning in childhood, including multiple cafe au lait macules, axillary and inguinal freckling, cutaneous and plexiform neurofibromas, iris hamartomas (known as Lisch nodules), and increased lifetime risk to develop optic glioma, other brain tumors, malignant peripheral nerve sheath tumors, and breast cancer.(1) NF1 has also been associated with learning disabilities, vasculopathy, and musculoskeletal features such as osteopenia, long bone dysplasia, and scoliosis.(1) Almost half of all individuals with NF1 have no family history as their variants arose de novo, during gamete formation or early embryogenesis.(1)

Of note, some individuals may present with segmental/mosaic NF1, where an NF1 variant may be localized to only one segment or a few segments of the body. This test may not detect mosaic NF1.(1)

The National Comprehensive Cancer Network provides recommendations regarding the breast cancer surveillance of adults with NF1.(2) Other medical management guidelines have been published by the American Academy of Pediatrics and the American College of Medical Genetics.(3,4)

Reference Values

An interpretive report will be provided.

Interpretation

All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(5) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Method Description

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 NF1 gene, 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 deletion-insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction-based quantitative method is performed to test for the presence of deletions and duplications in the NF1 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.

The reference transcript for NF1 gene is NM_000267.3. Reference transcript numbers may be updated due to transcript re-versioning. Always refer to the final patient report for gene transcript information referenced at the time of testing.(Unpublished Mayo method)

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

Day(s) Performed