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Genetic testing for Neurofibromatosis

Policy Number: MP-620

Latest Review Date:  February 2019

Category:  Laboratory                                                                    

Policy Grade: C

DESCRIPTION OF PROCEDURE OR SERVICE:

The neurofibromatoses are autosomal dominant genetic disorders associated with tumors of the peripheral and central nervous systems. There are three clinically and genetically distinct forms: neurofibromatosis (NF) Type 1 (NF1), NF Type 2 (NF2), and schwannomatosis. The potential benefit of genetic testing for NF is to confirm the diagnosis in an individual with suspected NF who does not fulfill diagnostic clinical criteria, or to determine future risk of NF in asymptomatic at-risk relatives.

Neurofibromatosis

There are three major clinically and genetically distinct forms of neurofibromatosis (NF): NF Type 1 (NF1; also known as von Recklinghausen disease), NF Type 2 (NF2), and schwannomatosis.

Neurofibromatosis Type 1

NF1 is one of the most common dominantly inherited genetic disorders, with an incidence at birth of one in 3000 individuals.

Clinical Characteristics

The clinical manifestations of NF1 show extreme variability, between unrelated individuals, among affected individuals within a single family, and within a single person at different times in life.

NF1 is characterized by multiple café-au-lait spots, axillary and inguinal freckling, multiple cutaneous neurofibromas, and iris Lisch nodules. It is referred to as segmental NF1 when limited to one area of the body. Many individuals with NF1 only develop cutaneous manifestations of the disease and Lisch nodules.

Cutaneous Manifestations

Café-au-lait spots occur in nearly all affected individuals and intertriginous freckling occurs in almost 90%. Café-au-lait spots are common in the general population, but when more than six are present, NF1 should be suspected. Café-au-lait spots are often present at birth and increase in number during the first few years of life.

Neurofibromas

Neurofibromas are benign tumors of Schwann cells that affect virtually any nerve in the body and develop most people with NF1. They are divided into cutaneous and plexiform types. Cutaneous neurofibromas, which develop in almost all people with NF1, are discrete, soft, sessile, or pedunculated tumors. Discrete cutaneous and subcutaneous neurofibromas are rare before late childhood. They may vary from a few to hundreds or thousands, and the rate of development may vary greatly from year to year. Cutaneous neurofibromas do not carry a risk of malignant transformation, but may be a major cosmetic problem in adults.

Plexiform neurofibromas, which occur in about half of individuals with NF1, are more diffuse growths that may be locally invasive. They can be superficial or deep and, therefore, the extent cannot be determined by clinical examination alone; magnetic resonance imaging (MRI) is the method of choice for imaging plexiform neurofibromas. Plexiform neurofibromas represent a major cause of morbidity and disfigurement in individuals with NF1. They tend to develop and grow in childhood and adolescence and then stabilize throughout adulthood. Plexiform neurofibromas can compress the spinal cord or airway and can transform into malignant peripheral nerve sheath tumors (MPNST). MPNST occur in approximately 10% of affected individuals.

Central Nervous System Tumors

Optic gliomas, which can lead to blindness, develop in the first six years of life. Symptomatic optic gliomas usually present before six years of age with loss of visual acuity or proptosis, but they may not become symptomatic until later in childhood or in adulthood.

While optic pathway gliomas are particularly associated with NF1, other CNS tumors occur at higher frequency in NF1, including astrocytomas and brainstem gliomas.

Other Findings

Other findings in NF1 include:

  • Intellectual disability occurs at a frequency of about twice that in the general population, and features of autism spectrum disorder occur in up to 30% of children with NF1.

  • Musculoskeletal features include dysplasia of the long bones, most often the tibia and fibula, which is almost always unilateral. Generalized osteopenia is more common in people with NF1 and osteoporosis is more common and occurs at a younger age than in the general population.1

  • Cardiovascular involvement includes the common occurrence of hypertension. Vasculopathies may involve major arteries or arteries of the heart or brain and can have serious or fatal consequences. Cardiac issues include valvar pulmonic stenosis, and congenital heart defects and hypertrophic cardiomyopathy may be especially frequent in individuals with NF1 whole gene deletions. Adults may develop pulmonary hypertension, often in association with parenchymal lung disease.

  • Lisch nodules are innocuous hamartomas of the iris.

Diagnosis

Although the clinical manifestations of NF1 are extremely variable and some are age-dependent, the diagnosis can usually made on clinical findings, and genetic testing is rarely needed for diagnosis.

The clinical diagnosis of NF1 should be suspected in individuals with the diagnostic criteria for NF1 developed by the National Institute of Health (NIH). The criteria are met when an individual has two or more of the following features:

  • Six or more café-au-lait macules over 5mm in greatest diameter in prepubertal individuals and over 15mm in postpubertal individuals

  • Two or more neurofibromas of any type or one plexiform neurofibroma

  • Freckling in the axillary or inguinal regions

  • Optic glioma

  • Two or more Lisch nodules (raised, tan-colored hamartomas of the iris)

  • A distinctive osseous lesion such as sphenoid dysplasia or tibial pseudoarthrosis

  • A first degree relative with NF1 as defined by the above criteria.

In adults, the clinical diagnostic criteria are highly specific and sensitive for a diagnosis of NF1.

Approximately half of children with NF1 and no known family history of NF1 meet NIH criteria for the clinical diagnosis by age one year. Almost all do by age eight years of age because many features of NF1 increase in frequency with age. Children who have inherited NF1 from an affected parent can usually be diagnosed within the first year of life because the diagnosis requires one diagnostic clinical feature in addition to a family history of the disease. This feature is usually multiple café-au-lait spots, present in infancy in more than 95% of individuals with NF1.

Young children with multiple café-au-lait spots and no other features of NF1 who do not have a parent with signs of NF1 should be suspected of having NF1, and followed clinically as if they do. A definitive diagnosis of NF1 can be made in most children by four years of age using NIH criteria.

Genetics

NF1 is caused by dominant loss-of-function mutations in the NF1 gene, which is a tumor suppressor gene located at chromosome 17q11.2 that encodes neurofibromin, a negative regulator of RAS activity. About half of affected individuals have a de novo NF1 variant. Penetrance is virtually complete after childhood, though expressivity is highly variable.

The variants responsible for NF1 are heterogeneous, and include nonsense and missense single nucleotide changes, single base insertions/deletions, splicing mutations (~30% of cases), whole gene deletions (~5% of cases), intragenic copy number variants, and other structural rearrangements. Several thousand pathogenic NF1 mutations have been identified, and none is frequent.

Management

Patient management guidelines for NF1 have been developed by the American Academy of Pediatrics, the National Society of Genetic Counselors and other expert groups.

After an initial diagnosis of NF1, the extent of the disease should be established, with personal medical history and physical examination and particular attention to features of NF1, ophthalmologic evaluation including slit lamp examination of the irides, developmental assessment in children, and other studies as indicated on the basis of clinically apparent signs or symptoms.

Surveillance recommendations for an individual with NF1 are for regular annual visits to include skin examination for new peripheral neurofibromas, signs of plexiform neurofibroma or progression of existing lesions, checks for hypertension, other studies (e.g., MRI) as indicated based on clinically apparent signs or symptoms, and monitoring of abnormalities of the central nervous system, skeletal system, or cardiovascular system by an appropriate specialist. In children, recommendations are for annual ophthalmologic examination in early childhood (less frequently in older children and adults), and regular developmental assessment.

Long-term care for individuals with NF1 aims at early detection and symptomatic treatment of complications.

It is recommended that radiotherapy be avoided, if possible, because radiotherapy in individuals with NF1 appears to be associated with a high risk of developing MPNST within the field of treatment.

Legius Syndrome

Clinical Characteristics

A few clinical syndromes may have clinical overlap with NF1, including Proteus syndrome, Noonan syndrome, McCune-Albright syndrome, and LEOPARD syndrome, but in most cases patients will be missing key features or will have features of the alternative disorder. However, Legius syndrome is a rare autosomal dominant disorder characterized but multiple café-au-lait macules, intertriginous freckling, macrocephaly, lipomas, and potential attention deficit-hyperactivity disorder. Misdiagnosis of Legius syndrome as NF1 might result in overtreatment and psychological burden on families with regard to potential serious neurofibromatosis related complications.

Genetics

Legius syndrome is associated with pathogenic loss-of-function variants in the SPRED1 gene on chromosome 15, which is the only known gene associated with Legius syndrome.

Management

Legius syndrome typically follows a benign course and management generally focuses on treatment of manifestations and prevention of secondary complications. Treatment of manifestations includes behavioral modification and/or pharmacologic therapy for those with ADHD; physical, speech, and occupational therapy for those with identified developmental delays; and individualized education plans for those with learning disorders.

Neurofibromatosis Type 2

NF2 (also known as bilateral acoustic neurofibromatosis and central neurofibromatosis) is estimated to occur in one in 33,000 individuals.

Clinical Characteristics

NF2 is characterized by bilateral vestibular schwannomas and associated symptoms of tinnitus, hearing loss, and balance dysfunction. Average age of onset is 18 to 24 years, and almost all affected individuals develop bilateral vestibular schwannomas by age 30 years. Affected individuals may also develop schwannomas of other cranial and peripheral nerves, ependymomas, meningioma, and, rarely, astrocytoma. The most common ocular finding, which may be the first sign of NF2, is posterior subcapsular lens opacities; they rarely progress to visually significant cataracts.

Most patients with NF2 present with hearing loss, which is usually unilateral at onset. Hearing loss may be accompanied or preceded by tinnitus. Occasionally, features such as dizziness or imbalance are the first symptom. A significant proportion of cases (20%-30%) present with an intracranial meningioma, spinal, or cutaneous tumor. The presentation in the pediatric population may differ from the adult population, in that, in children, vestibular schwannomas may account for as little as 15% to 30% of initial symptoms.

Diagnosis

The diagnosis of NF2 is usually made on clinical findings. Modified NIH diagnostic clinical criteria are one of the following:

  • Bilateral vestibular schwannomas

  • A first-degree relative with NF2 AND

    • Unilateral vestibular schwannoma OR

    • Any two of: meningioma, schwannoma, glioma, neurofibroma, posterior subcapsular lenticular opacities.

  • Multiple meningiomas AND

    • Unilateral vestibular schwannoma OR

    • Any two of: schwannoma, glioma, neurofibroma, cataract.

Genetics

NF2 is inherited in an autosomal dominant manner; approximately 50% of individuals have an affected parent and the other 50% have NF2 as a result of a de novo mutation.

Between 25% and 33% of individuals with NF2 caused by a de novo mutation have somatic mosaicism. Variant detection rates are lower in simplex cases and in an individual in the first generation of a family to have NF2 because they are more likely to have somatic mosaicism. Somatic mosaicism can make clinical recognition of NF2 difficult and results in lower mutation detection rates. Clinical recognition of NF2 in these patients may be more difficult because these individuals may not have bilateral vestibular schwannomas. Variant detection rates may be lower because molecular genetic testing may be normal in unaffected tissue (e.g., lymphocytes), and molecular testing of tumor tissue may be necessary to establish the presence of somatic mosaicism.

Management

In an individual diagnosed with NF2, it is recommended that an initial evaluation establish the extent of the disease, typically using head MRI, hearing evaluation, and ophthalmologic and cutaneous examinations.

Counseling is recommended for insidious problems with balance and underwater disorientation, which can result in drowning.

Hearing preservation and augmentation are part of the management of NF2, as is early recognition and management of visual impairment from other manifestations of NF2. Therefore, routine hearing and eye examination should be a part of care of individuals with NF2.

Surveillance measures for affected or at-risk individuals include annual MRI beginning at around age 10 and continuing until at least the fourth decade of life.

Treatment of manifestations includes surgical resection of small vestibular schwannomas, which may often be completely resected with preservation of hearing and facial nerve function. Larger tumors are often managed expectantly with debulking or decompression when brain stem compression, deterioration of hearing, and/or facial nerve dysfunction occurs.

Radiotherapy should be avoided, because radiotherapy of NF2-associated tumors, especially in childhood, may induce, accelerate, or transform tumors.

Evaluation of At-Risk Relatives

Early identification of relatives who have inherited the family-specific NF2 mutation allows for appropriate screening using MRI for neuroimaging and audiologic evaluation, which result in earlier detection and improved outcomes. Identification of at-risk relatives who do not have the family-specific NF2 mutation eliminates the need for surveillance.

Schwannomatosis

Schwannomatosis is a rare condition that is defined as multiple schwannomas without vestibular schwannomas that are diagnostic of NF2. Individuals with schwannomatosis may develop intracranial, spinal nerve root, or peripheral nerve tumors. Familial cases are inherited in an autosomal dominant manner, with highly variable expressivity and incomplete penetrance. Clinically, schwannomatosis is distinct from NF1 and NF2, although some individuals eventually fulfill diagnostic criteria for NF2. SMARCB1 variants have been shown to cause 30% to 60% of familial schwannomatosis but only a small number of simplex disease.

POLICY:

Genetic testing for neurofibromatosis may be considered medically necessary when the diagnosis is clinically suspected due to signs of disease, but a definitive diagnosis cannot be made without genetic testing.

Genetic testing for neurofibromatosis in at-risk relatives with no signs of disease may be considered medically necessary when a definitive diagnosis cannot be made without genetic testing AND at least ONE of the following criteria is met:

  • A close relative (i.e. first, second, or third degree relative) has a known NF mutation; OR

  • A close relative has been diagnosed with neurofibromatosis but whose genetic status is unavailable.

Genetic testing for neurofibromatosis is considered not medically necessary and investigational for all other situations not meeting the criteria outlined above.

KEY POINTS:

The most recent literature was updated through October 30, 2018.

Evidence reviews assess whether a medical test is clinically useful. A useful test provides information to make a clinical management decision that improves the net health outcome. That is, the balance of benefits and harms is better when the test is used to manage the condition than when another test or no test is used to manage the condition.

The first step in assessing a medical test is to formulate the clinical context and purpose of the test. The test must be technically reliable, clinically valid, and clinically useful for that purpose. Evidence reviews assess the evidence on whether a test is clinically valid and clinically useful. Technical reliability is outside the scope of these reviews, and credible information on technical reliability is available from other sources.

Schwannomatosis is rare and far less well-described than neurofibromatosis Type 1 (NF1) and neurofibromatosis Type 2 (NF2); therefore, this review will focus on NF1 and NF2.

Neurofibromatosis

Clinical Context and Test Purpose

The purpose of genetic testing in patients who have suspected NF is to inform a decision to pursue additional surveillance for comorbid conditions as recommended by well-defined management guidelines, if a definitive diagnosis can be made.

The question addressed in this evidence review is: For individuals who have suspected NF or who are asymptomatic with a close relative(s) with an NF diagnosis, does the use of genetic testing result in improved patient outcomes?

The following PICOTS were used to select literature to inform this review.

Patients

The relevant populations of interest are individuals with suspected NF1 or NF2, based on clinical symptoms or because of a family member with a diagnosis of NF1 or NF2.

Intervention

Interventions considered include are genetic tests of NF1, NF2, and SPRED1 variants.

Comparator

The following tool is currently being used to make diagnostic decisions about suspected NF1 and NF2: Currently, clinical decision about NF1 and NF2 is being made using NIH diagnostic criteria.

Outcomes

The potential beneficial outcomes of primary interest include earlier intervention and improved outcomes, and direct clinical management according to accepted guideline recommendations.

Harmful outcomes resulting from a false positive test result include the potential for unneeded additional tests, while false negative tests could lead to a delay in care.

Timing

The duration of follow up is years for the non-test-related outcomes.

Setting

These tests would typically be ordered by a specialist. Genetic counseling is an important component of care delivery.

Study Selection Criteria

Methodologically credible studies were selected using the following principles:

  • To assess the clinical validity of genetic testing to evaluate neurofibromatosis, studies should report variant detection rates.
  • To assess the clinical utility of genetic testing to evaluate neurofibromatosis, studies should demonstrate how results of the genetic tests impact treatment decisions and overall management of the patient.

Technically Reliable

Assessment of technical reliability focuses on specific tests and operators and requires review of unpublished and often proprietary information. Review of specific tests, operators, and unpublished data are outside the scope of this evidence review and alternative sources exist. This evidence review focuses on the clinical validity and clinical utility.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Neurofibromatosis Type 1

Detecting mutation in the NF1 gene is challenging because of the gene’s large size, the lack of mutation hotspots, and the wide variety of possible lesions.

A multistep variant testing protocol identifies more than 95% of NF1 pathogenic variants in individuals who fulfill the National Institutes of Health (NIH) diagnostic criteria. The protocol involves sequencing of both mRNA (cDNA) and genomic DNA, and testing for whole NF1 deletions (e.g., by MLPA) because whole gene deletions cannot be detected by sequencing. Due to the wide variety and rarity of individual pathogenic mutation variants in NF1, sequencing of cDNA increases the detection rate of variants from approximately 61% with genomic DNA sequence analysis alone to greater than 95% with sequencing for both cDNA and genomic DNA and testing for whole gene deletions. 

Table 1 summarizes several studies conducted on various populations, using various testing techniques to detect NF1 and SPRED variants. Below is a detailed description of two of the studies with high variant detection rates.

Sabbagh et al (2013) reported a comprehensive mutation analysis of constitutional NF1 variants in unrelated, well-phenotyped index cases with typical clinical features of NF1 who enrolled in a French clinical research program. The 565 families for this study (N=1697 individuals) were enrolled between 2002 and 2005; 1083 fulfilled NIH diagnostic criteria for NF1. A comprehensive NF1 variant screening (sequencing of both cDNA and genomic DNA, as well as large deletion testing by MLPA) was performed in 565 individuals, one from each family, who had a sporadic variant or who represented the familial index case. A NF1 variant was identified in 546, a variant detection rate of 97%. A total of 507 alterations were identified at the cDNA and genomic DNA levels. Among these 507 alterations, 487 were identified using only the genomic DNA sequencing approach and 505 were identified using the single cDNA sequencing approach. MLPA detected 12 deletions/duplications that would not have been detected by sequencing. No variant was detected in 19 patients (3.4%), two of whom had a SPRED1 mutation, which is frequently confused with NF; the remainder may have been due to an unknown mutation of the NF1 locus.

Valero et al (2011) developed a method for detecting NF1 variants by combining an RNA-based cDNA-polymerase chain reaction mutation detection method and denaturing high-performance liquid chromatography with MLPA. Their protocol was validated in a cohort of 56 patients with NF1 (46 sporadic cases, 10 familial cases) who fulfilled NIH diagnostic criteria. A variant was identified in 53 cases (95% sensitivity), involving 47 different variants, of which 23 were novel. After validation, the authors implemented the protocol as a routine test and subsequently reported the spectrum of NF1 variants identified in 93 patients in a cohort of 105. The spectrum included a wide variety of variants (nonsense, small deletions or insertions/duplications, splice defects, complete gene deletions, missense, single exon deletions and duplications, and a multiexon deletion), confirming the heterogeneity of the NF1 gene mutations that can cause NF1.

Table 1. Diagnostic Performance of Genetic Testing for Suspected NF1

Study

N

Population

Test Description

Results

Zhu et al (2016)

32

NF1 patients (plus 120 population match controls)

PCR sequencing of NF1 gene, followed by MLPA

93.8% (30/32) patients had NF1 variant detected

Zhang et al (2015)

109

Patients with NF1-like phenotypes

Sanger sequencing, MLPA, and cDNA of NF1, in sequence; followed by Sanger sequencing and MLPA of SPRED1 if all others negative (n=14)

NF1 variant detected in:

  • 89% (89/100) of NF1 probands

  • 93% (70/75) of patients who met NIH criteria for NF1

Bianchessi et al (2015)

293

Patients meeting NIH NF1 criteria

MLPA, aCGH, DHPLC, and Sanger sequencing, in sequence, of NF1

70% had NF1 variant detected

150

Patients with NF1-like symptoms without meeting NIH criteria

MLPA, aCGH, DHPLC, and Sanger sequencing, in sequence, of NF1

22% had NF1 variant detected

61

Patients meeting NIH criteria

MLPA followed by RNA sequencing of NF1

87% had NF1 variant detected

9

Patients with NF1-like symptoms without meeting NIH criteria

MLPA followed by RNA sequencing of NF1

33.3% had NF1 variant detected

Spurlock et al (2009)

85

Patients with NF1-like phenotypes (mild), with negative NF1 testing

PCR sequencing of SPRED1

6 SPRED variants detected

Valero et al (2011)

56

Unrelated, well-phenotyped index cases with typical clinical features of NF1

NF1 variant screening (sequencing of both cDNA and genomic DNA, as well as large deletion testing by MLPA)

97% (546/565) patients had NF1 variant detected

Sabbagh et

al (2013)

565

Unrelated, well-phenotyped index cases with typical clinical features of NF1

NF1 variant screening (sequencing of both cDNA and genomic DNA, as well as large deletion testing by MLPA)

97% (546/565) patients had NF1 variant detected

Zhang et al

(2015)

109

Patients with NF1-like phenotypes

Sanger sequencing, MLPA, and cDNA of NF1, in sequence; followed by Sanger sequencing and MLPA of SPRED1 if all others negative (n=14)

NF1 variant detected in:

  • 89% (89/100) of NF1 probands

  • 93% (70/75) of patients met NIH criteria for NF1

Cali et al

(2017)

79

Patients in Italy with

suspected or clinically

diagnosed NF1

NGS using Ion Torrent PGM Platform followed by MLPA and calculation of mosaicism

percentage using Sanger sequencing

73 variants were identified in 79 NF1 patients

aCGH: array comparative genomic hybridization; DHPLC: denaturing high pressure liquid chromatography; MLPA: multiplex ligation-dependent probe amplification; NF1: neurofibromatosis Type 1; NGS: next-generation sequencing; NIH: National Institutes of Health; PCR: polymerase chain reaction.

Genotype-Phenotype Correlations

NF1 is characterized by extreme clinical variability between unrelated individuals, among affected individuals within a single family and even within a single person with NF1 at different times in life. Only two clear correlations have been observed between certain NF1 alleles and consistent clinical phenotypes:

  1. A deletion of the entire NF1 gene is associated with large numbers and early appearance of cutaneous neurofibromas, more frequent and severe cognitive abnormalities, somatic overgrowth, large hands and feet, and dysmorphic facial features.

  2. A three base pair in-frame deletion of exon 17 is associated with typical pigmentary features of NF1, but no cutaneous or surface plexiform neurofibromas.

In addition, missense mutations of NF1 p.Arg1809 have been associated typical NF1 findings of multiple café-au-lait macules and axillary freckling but reduced frequency of NF1-associated benign or malignant tumors. In one cohort of 136 patients, patients had features of Noonan syndrome (i.e., short stature, pulmonic stenosis) present in excess (26.2%).

In the Sabbagh et al (2013) study described above, the authors evaluated genotype-phenotype correlations for a subset of patients. This subset included 439 patients harboring a truncating (n=368), in-frame splicing (n=36), or missense (n=35) NF1 variant to assess the contribution of intragenic NF1 variants (vs large gene deletions) to the variable expressivity of NF1. Their findings suggested a tendency for truncating variants to be associated with a greater incidence of Lisch nodules and a larger number of café-au-lait spots compared with missense variants.

However, other studies (e.g., Zhu et al [2016], shown in Table 1; Hutter et al [2016]; Ko et al [2013]) report no association between mutation type and phenotype.

Legius Syndrome

In 2009, Pasmant et al described a cohort of 61 index cases meeting the NIH clinical diagnosis of NF1 but without an identifiable NF1 variant detectable who were screened for germline loss-of-function variants in the SPRED1 gene, located on 15q13.2. SPRED1 variants were detected in 5% of patients with NF1 features, which were characterized by café-au-lait macules and axillary and groin freckling but not neurofibromas and Lisch nodules. The authors characterized a new syndrome (Legius syndrome) based on the presence of a heterozygous SPRED1 variant.

Also in 2009, Messian et al described a separate cohort of 22 NF1-variant negative probands who met NIH clinical criteria for NF1 with a SPRED1 loss-of-function variant who participated in genotype-phenotype testing with their families. Forty patients were found to be SPRED1 variant positive, 20 (50%, 95% CI 34% to 66%) met NIH clinical criteria for NF1, although none had cutaneous or plexiform neurofibromas, typical NF osseous lesions, or symptomatic optic pathway gliomas. The authors also reported on an anonymous cohort of 1,318 samples received at the UAB Genomics Laboratory for NF1 genetic testing from 2003 to 2007 if a phenotypic checklist of NF-related symptoms had been filled out by the referring physician. In the anonymous cohort, 26 pathogenic SPRED1 variants in 33 probands were identified. Of 1,086 patients fulfilling NIH criteria for a clinical diagnosis of NF1, a SPRED1 variant was identified in 21 (1.9%, 95% CI 1.2% to 2.9%).

Neurofibromatosis Type 2

At least 200 different NF2 variants have been described, most of which are point variants. Large deletions of NF2 represent 10% to 15% of NF2 variants. When variant scanning is combined with deletion/duplication analysis of single exons, the variant detection rate approaches 72% in simplex cases and exceeds 92% for familial cases. Wallace et al (2005) applied neurofibromatosis type 2 mutation scanning for the NF2 gene to 271 patient samples (245 lymphocyte DNA, 26 schwannoma DNA). The overall NF2 variant detection rate was 88% among familial cases and 59% among sporadic cases. Evans et al (2007) analyzed database of 460 families with NF2 and 704 affected individuals for mosaicism and transmission risks to offspring. The authors identified a variant in 84 (91%) of 92 second-generation families, with a sensitivity of greater than 90%. Other studies have reported lower variant detection rates, which likely reflects the inclusion of more mildly affected individuals with somatic mosaicism.

Genotype-Phenotype Correlations

Intrafamilial variability is much lower than interfamilial variability, and the phenotypic expression and natural history of the disease are similar within families with multiple members with NF2.

Frameshift or nonsense variants cause truncated protein expression, which has been associated with more severe manifestations of NF2. Missense or in-frame deletions have been associated with milder manifestations of the disease. Large deletions of NF2 have been associated with a mild phenotype.

Selvanathan et al (2010) reported on genotype-phenotype correlations in 268 patients with an NF2 variant. Variants that resulted in a truncated protein were associated with statistically significant younger age at diagnosis, higher prevalence and proportion of meningioma’s, spinal tumors and tumors of cranial nerves other than VIII, vestibular schwannomas at a younger age, and more cutaneous tumors. Variants found in the later part of the gene, especially exons 14 and 15, were associated with milder disease and fewer meningioma.

Section Summary: Clinically Valid

Studies conducted among multiple cohorts of patients meeting NIH criteria for NF1 reported high sensitivity of multistep variant testing protocol in identifying pathogenic NF1 variants. On the other hand, studies conducted among familial and sporadic NF2 cases reported a variant detection rate exceeding 90% for familial cases and more than 70% in simplex cases.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, or more effective therapy, or avoid unnecessary therapy, or avoid unnecessary testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials.

No direct evidence was identified reporting on outcomes for genetic testing of individuals with suspected NF or at-risk relatives with a proband with NF.

Chain of Evidence

Indirect evidence on clinical utility rests on clinical validity. If the evidence is insufficient to demonstrate test performance, no inferences can be made about clinical utility. 

Individuals with Suspected NF

In many cases of suspected NF1, the diagnosis will be able to be made clinically based on the NIH criteria, which are both highly sensitive and specific, except in young children. However, there are suspected cases in children and adults who do not fulfill the NIH diagnostic criteria. Given the well-established clinical management criteria, these patients benefit from genetic testing to confirm the diagnosis and to direct clinical management according to accepted guideline recommendations.

For NF2, affected individuals may have little in the way of external manifestations and the onset of symptoms may be due to tumors other than vestibular schwannomas, particularly in children. Early identification of patients with NF2 can lead to earlier intervention and improved outcomes, and direct clinical management according to accepted guideline recommendations.

Subsection Summary: Individuals With Suspected NF

Currently, there is no direct evidence from studies demonstrating that genetic testing for NF1 and NF2 result in improved patient outcomes (e.g., survival or quality of life) among suspected cases. Suspected cases of NF1 or NF2 among children and adults who do not meet the NIH diagnostic criteria might benefit from genetic testing in confirming the diagnosis and receiving treatment, which might result in improved outcomes.

At-Risk Relatives

Similar to the case for suspected NF1, it is most of the case that a clinical diagnosis will be able to be made in an at-risk relative of a proband because, in that one of the NIH criterions for diagnosis is having a first-degree relative with NF1, and, therefore, only one other clinical sign is necessary for diagnosis. Cases in at-risk relatives who do not fulfill the NIH diagnostic criteria may benefit from genetic testing to direct clinical management according to accepted guideline recommendations.

Testing for NF2 may be useful to identify at-risk relatives of patients with an established diagnosis of NF2, allowing for appropriate surveillance, earlier detection, and treatment of disease manifestations, and avoiding unnecessary surveillance in an individual who does not have the family-specific mutation. Unlike NF1, the age of onset of symptoms of NF2 is relatively uniform within families. Therefore, it is usually not necessary to offer testing or surveillance to asymptomatic parents of a proband. However, testing of at-risk asymptomatic individuals younger than 18 years of age may be particularly useful, especially in children, to avoid unnecessary procedures in a child who has not inherited the variant.

Subsection Summary: At-Risk Relatives

Currently, there is no direct evidence from studies demonstrating that genetic testing for NF1 and NF2 result in improved outcomes (e.g., survival or quality of life) among asymptomatic individuals with a close relative(s) with a neurofibromatosis diagnosis. However, genetic testing of at-risk asymptomatic individuals not fulfilling clinical diagnostic criteria might benefit through diagnosis, clinical management if needed and in avoiding unnecessary procedures in case of individuals who have not inherited the variant.

Summary of Evidence

For individuals who have suspected NF who receive genetic testing for NF, the evidence includes clinical validation studies of a multistep diagnostic protocol and genotype-phenotype correlation studies. Relevant outcomes are test accuracy and validity, symptoms, morbid events, and functional outcomes. A multistep mutation testing protocol identifies more than 95% of pathogenic variants in NF1 and for NF2, the variant detection rate approaches 72% in simplex cases and exceeds 90% for familial cases. The evidence is sufficient to determine that the technology results in a meaningful improvement in the net health outcome.

For individuals who are asymptomatic with a close relative(s) with a NF diagnosis who receive genetic testing for NF, there is no direct evidence. Relevant outcomes are test accuracy and validity, symptoms, morbid events, and functional outcomes. For individuals with a known pathogenic variant in the family, testing of at-risk relatives will confirm or exclude the variant with high certainty. Direct evidence on the clinical utility of genetic testing for NF is lacking, but a definitive diagnosis resulting from genetic testing, can direct patient care according to established clinical management guidelines, including referrals to the proper specialists, treatment of manifestations, and surveillance. Testing of at-risk relatives will lead to initiation or avoidance of management and/or surveillance. Early surveillance may be particularly important for patients with NF2, because early identification of internal lesions by imaging is expected to improve outcomes. The evidence is sufficient to determine that the technology results in a meaningful improvement in the net health outcome.

Practice Guidelines and Position Statements

In 2008, the American Academy of Pediatrics published diagnostic and health supervision guidelines for children with NF1. The guidance states that “when there is uncertainty regarding a definitive diagnosis, for instance, in the presence of some of the clinical manifestations of NF1, such as only CLSs, but not enough to establish a clinical diagnosis, consideration should be given to seeking genetic consultation and determining whether genetic testing is indicated at that time to expedite a diagnosis.”

U.S. Preventive Services Task Force Recommendations

Not applicable.

KEY WORDS:

Neurofibromatosis 1, Neurofibromatosis 2, Neurofibromatosis, NF1, NF2, Genetic testing, Café-au-lait, Schwannomatosis, SPRED1, von Recklinghausen disease

APPROVED BY GOVERNING BODIES:

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory-developed tests (LDTs) must meet the general regulatory standards of the Clinical Laboratory Improvement Act (CLIA). Lab tests for neurofibromatosis are available under the auspices of CLIA. Laboratories that offer LDTs must be licensed by CLIA for high-complexity testing. To date, the U.S. Food and Drug Administration has chosen not to require any regulatory review of this test.

BENEFIT APPLICATION:

Coverage is subject to member’s specific benefits.  Group specific policy will supersede this policy when applicable.

ITS: Home Policy provisions apply.

FEP:  Special benefit consideration may apply.  Refer to member’s benefit plan.  FEP does not consider investigational if FDA approved and will be reviewed for medical necessity.

CURRENT CODING: 

CPT Codes:

81405

 NF2 (neurofibromin 2 [merlin]) (e.g., neurofibromatosis, type 2), duplication/deletion analysis

81406

 NF2 (neurofibromin 2 [merlin]) (e.g., neurofibromatosis, type 2), full gene sequence

81408

 NF1 (neurofibromin 1) (e.g., neurofibromatosis, type 1), full gene sequence

REFERENCES:

  1. ARUP Laboratories. Neurofibromatosis Type 1 (NF1) sequencing and deletion/duplication. 2016; //ltd.aruplab.com/Tests/Pub/2007154. Accessed January 2018.

  2. Bernier A, Larbrisseau A, Perreault S. Cafe-au-lait macules and neurofibromatosis type 1: a review of the literature. Pediatr Neurol. Jul 2016; 60:24-29 e21.

  3. Bianchessi D, Morosini S, Saletti V, et al. 126 novel mutations in Italian patients with neurofibromatosis type 1. Mol Genet Genomic Med. Nov 2015; 3(6):513-525.

  4. Cali F, Chiavetta V, Ruggeri G, et al. Mutation spectrum of NF1 gene in Italian patients with neurofibromatosis type 1 using Ion Torrent PGM platform. Eur J Med Genet. Feb 2017; 60(2):93-99.

  5. Evans DG, Sainio M, Baser ME. Neurofibromatosis type 2. J Med Genet. Dec 2000; 37(12):897-904.

  6. Evans DG. Neurofibromatosis 2. In: Adam MP, Ardinger HH, Pagon RA, et al., eds. GeneReviews. Seattle, WA: University of Washington; 2011.

  7. Evans DG. Neurofibromatosis 2. In: Pagon RA, Adam MP, Ardinger HH, et al., eds. GeneReviews(R). Seattle (WA); 1993.

  8. Evans DG. Neurofibromatosis type 2. In: UpToDate, ed. UpToDate. Waltham, MA; 2015.

  9. Evans DG, Ramsden RT, Shenton A, et al. Mosaicism in neurofibromatosis type 2: an update of risk based on uni/bilaterality of vestibular schwannoma at presentation and sensitive mutation analysis including multiple ligation-dependent probe amplification. J Med Genet. Jul 2007; 44(7):424-428.

  10. Friedman JM. Neurofibromatosis 1. In: Pagon RA, Adam MP, Ardinger HH, et al., eds. GeneReviews(R). Seattle (WA); 1993.

  11. Hersh JH. Health supervision for children with neurofibromatosis. Pediatrics. Mar 2008; 121(3):633-642.

  12. Hutter S, Piro RM, Waszak SM, et al. No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients. Hum Genet. May 2016; 135(5):469-475.

  13. Ko JM, Sohn YB, Jeong SY, et al. Mutation spectrum of NF1 and clinical characteristics in 78 Korean patients with neurofibromatosis Type 1. Pediatr Neurol. Jun 2013; 48(6):447-453.

  14. Mautner VF, Kluwe L, Friedrich RE, et al. Clinical characterisation of 29 neurofibromatosis type-1 patients with molecularly ascertained 1.4 Mb type-1 NF1 deletions. J Med Genet. Sep 2010; 47(9):623-630.

  15. Messiaen L, Yao S, Brems H, et al. Clinical and mutational spectrum of neurofibromatosis type 1-like syndrome. JAMA. Nov 18 2009; 302(19):2111-2118.

  16. Pasmant E, Sabbagh A, Hanna N, et al. SPRED1 germline mutations caused a neurofibromatosis type 1 overlapping phenotype. J Med Genet. Jul 2009; 46(7):425-430.

  17. Pasmant E, Sabbagh A, Spurlock G, et al. NF1 microdeletions in neurofibromatosis type 1: from genotype to phenotype. Hum Mutat. Jun 2010; 31(6):E1506-1518.

  18. Pinna V, Lanari V, Daniele P, et al. p.Arg1809Cys substitution in neurofibromin is associated with a distinctive NF1 phenotype without neurofibromas. Eur J Hum Genet. Aug 2015; 23(8):1068-1071.

  19. Rojnueangnit K, Xie J, Gomes A, et al. High incidence of Noonan syndrome features including short stature and pulmonic stenosis in patients carrying NF1 missense mutations affecting p.Arg1809: genotypephenotype correlation. Hum Mutat. Nov 2015; 36(11):1052-1063.

  20. Sabbagh A, Pasmant E, Imbard A, et al. NF1 molecular characterization and neurofibromatosis type I genotype-phenotype correlation: the French experience. Hum Mutat. Nov 2013; 34(11):1510-1518.

  21. Selvanathan SK, Shenton A, Ferner R, et al. Further genotype--phenotype correlations in neurofibromatosis 2. Clin Genet. Feb 2010; 77(2):163-170.

  22. Spurlock G, Bennett E, Chuzhanova N, et al. SPRED1 mutations (Legius syndrome): another clinically useful genotype for dissecting the neurofibromatosis type 1 phenotype. J Med Genet. Jul 2009; 46(7):431- 437.

  23. Stevenson D, Viskochil D, Mao R. Legius Syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al., eds. GeneReviews. Seattle, WA: University of Washington; 2015.

  24. Upadhyaya M, Huson SM, Davies M, et al. An absence of cutaneous neurofibromas associated with a 3-bp inframe deletion in exon 17 of the NF1 gene (c.2970-2972 delAAT): evidence of a clinically significant NF1 genotype-phenotype correlation. Am J Hum Genet. Jan 2007; 80(1):140-151.

  25. Valero MC, Martin Y, Hernandez-Imaz E, et al. A highly sensitive genetic protocol to detect NF1 mutations. J Mol Diagn. Mar 2011; 13(2):113-122.

  26. van Minkelen R, van Bever Y, Kromosoeto JN, et al. A clinical and genetic overview of 18 years neurofibromatosis type 1 molecular diagnostics in the Netherlands. Clin Genet. Apr 2014; 85(4):318-327.

  27. Wallace AJ, Watson CJ, Oward E, et al. Mutation scanning of the NF2 gene: an improved service based on meta-PCR/sequencing, dosage analysis, and loss of heterozygosity analysis. Genet Test. Winter 2004; 8(4):368- 380.

  28. Zhang J, Tong H, Fu X, et al. Molecular characterization of NF1 and neurofibromatosis type 1 genotypephenotype correlations in a Chinese population. Sci Rep. Jun 09 2015; 5:11291.

  29. Zhu L, Zhang Y, Tong H, et al. Clinical and molecular characterization of NF1 patients: single-center experience of 32 patients from China. Medicine (Baltimore). Mar 2016; 95(10):e3043.

POLICY HISTORY:

Medical Policy Group, July 2010

Medical Policy Group, April 2011

Medical Policy Group, February 2012

Medical Policy Group, February 2013

Medical Policy Group, January 2014

Medical Policy Panel, January 2016

Medical Policy Group, February 2016 (3): removed all aspects of genetic testing for Neurofibromatosis from medical policy #136 and created separate policy; Updated literature, Key Words & References; no change in policy statement 

Medical Policy Panel, January 2017

Medical Policy Group, February 2017 (3): 2017 Updates to Description, Key Points, Key Words, & References; no change to Policy statements

Medical Policy Panel, January 2018

Medical Policy Group, January 2018 (3): 2018 Updates to Description, Key Points, & References; no change to policy statement.

Medical Policy Panel, January 2019

Medical Policy Group, February 2019 (9): 2019 Updates to Description and Key Points. No change to policy statement.

 


This medical policy is not an authorization, certification, explanation of benefits, or a contract. Eligibility and benefits are determined on a case-by-case basis according to the terms of the member’s plan in effect as of the date services are rendered. All medical policies are based on (i) research of current medical literature and (ii) review of common medical practices in the treatment and diagnosis of disease as of the date hereof. Physicians and other providers are solely responsible for all aspects of medical care and treatment, including the type, quality, and levels of care and treatment.

This policy is intended to be used for adjudication of claims (including pre-admission certification, pre-determinations, and pre-procedure review) in Blue Cross and Blue Shield’s administration of plan contracts.

The plan does not approve or deny procedures, services, testing, or equipment for our members. Our decisions concern coverage only. The decision of whether or not to have a certain test, treatment or procedure is one made between the physician and his/her patient. The plan administers benefits based on the member’s contract and corporate medical policies. Physicians should always exercise their best medical judgment in providing the care they feel is most appropriate for their patients. Needed care should not be delayed or refused because of a coverage determination.

As a general rule, benefits are payable under health plans only in cases of medical necessity and only if services or supplies are not investigational, provided the customer group contracts have such coverage.

The following Association Technology Evaluation Criteria must be met for a service/supply to be considered for coverage:

1. The technology must have final approval from the appropriate government regulatory bodies;

2. The scientific evidence must permit conclusions concerning the effect of the technology on health outcomes;

3. The technology must improve the net health outcome;

4. The technology must be as beneficial as any established alternatives;

5. The improvement must be attainable outside the investigational setting.

Medical Necessity means that health care services (e.g., procedures, treatments, supplies, devices, equipment, facilities or drugs) that a physician, exercising prudent clinical judgment, would provide to a patient for the purpose of preventing, evaluating, diagnosing or treating an illness, injury or disease or its symptoms, and that are:

1. In accordance with generally accepted standards of medical practice; and

2. Clinically appropriate in terms of type, frequency, extent, site and duration and considered effective for the patient’s illness, injury or disease; and

3. Not primarily for the convenience of the patient, physician or other health care provider; and

4. Not more costly than an alternative service or sequence of services at least as likely to produce equivalent therapeutic or diagnostic results as to the diagnosis or treatment of that patient’s illness, injury or disease.