Coverage Policy Manual
Policy #: 2013025
Category: Medicine
Initiated: August 2013
Last Review: June 2018
  Genetic Test: CHARGE Syndrome

Description:
CHARGE syndrome is a rare genetic condition associated with multiple congenital anomalies. In many individuals, the diagnosis can be made based on clinical findings. However, the phenotype of the disease is highly variable, and some patients do not fulfill the criteria for a definite diagnosis by clinical findings. Sequence analysis of the CHD7 coding region detects mutations in most individuals with CHARGE syndrome.
 
Description of the disease
CHARGE syndrome is a rare genetic condition caused by mutations of the CHD7 gene on chromosome 8q12.1. The letters of CHARGE syndrome correspond to clinical features: C = ocular Coloboma, H = Heart defect, A = Atresia choanae, R = Retarded growth and development, G = Genital hypoplasia, and E = Ear anomalies/deafness. However, a number of other malformations are also common in this condition. In particular, hypoplasia of the semi-circular canals has emerged as a frequent and distinctive CHARGE malformation.
 
Newborns with CHARGE syndrome typically have a several major congenital malformations that affect vision, hearing, cardiovascular function, growth, development, neurologic function, and overall well-being. Mortality is relatively high in neonates with bilateral choanal atresia, cyanotic cardiac malformations, CNS malformations, and/or tracheoesophageal fistula. In one series, the death rate was 20% in the first month of life and about 50% by 6 months of age (Tellier, 1998).  A formal epidemiologic study in Canada concluded that those who survived infancy were likely to have long-term survival (Issekutz, 2005). Morbidity is chronic and multi-systemic. Cognitive outcome is difficult to assess because both motor skills and language do not necessarily reflect intellect in this group. About 75% have some degree of intellectual disability. Among the 25% with normal intelligence, many are well-educated and live independently as adults (Lalani, 1993l Bergman, 2011).
 
In addition, investigators have conducted an extended debate about the relative importance of certain clinical signs. Consequently, the diagnostic criteria for CHARGE syndrome have been repeatedly revised.
 
Clinical diagnosis of CHARGE syndrome
The complete phenotypic spectrum of CHARGE was only revealed after identification of the causative gene in 2004, and the phenotypic spectrum of the disease is highly variable.
 
A 2012 review (Lalani, 2012) proposes that the diagnosis of CHARGE syndrome be considered definite if an individual has four major characteristics or 3 major and 3 minor characteristics, as initially proposed by Blake et al in 1998 (the Blake criteria), and described below (Blake, 1998).
 
Major characteristics
 
Ocular coloboma, which may be manifest in the iris and/or the retina, choroid, and optic disc, and sometimes as microphthalmia. [Present in 80-90% of affected individuals]
 
Choanal atresia or stenosis, which may be unilateral or bilateral. Complete bilateral choanal atresia is a life-threatening emergency in a newborn, since neonates are obligate nose breathers. Some CHARGE patients have a cleft palate, in which case the cleft fulfills this criterion. [50-60%]
 
Cranial nerve abnormality, including hyposmia or anosmia (CN I), facial palsy (CN VII), auditory nerve hypoplasia causing sensorineural hearing loss (CN VIII), and/or swallowing problems [70-90%] with or without aspiration (CN IX and CN X).
 
Characteristic auditory manifestation of the external, middle, or inner ear. [80-100%] The external ear is often dysmorphic. A number of ossicular malformations of the middle ear are common. Sensorineural hearing loss is associated with a Mondini malformation of the cochlea, and vestibular dysfunction is caused by aplasia or hypoplasia of the semicircular canals in 95% of individuals with CHARGE. Temporal bone CT is necessary to diagnose the cochlear and semicircular canal defects.
 
Minor characteristics
Genital hypoplasia in boys is manifest as micropenis and cryptorchidism, and in girls as hypoplasic labia. Puberty may be delayed because of hypogonadotrophic hypogonadism. [50%]
 
Developmental delays, especially gross motor and language delays, which may be intrinsic qualities or caused by impaired balance, deafness, blindness, hypotonia, surgery, or other chronic illness. [100%]
 
Congenital cardiac malformations. [80%]
 
Short stature, often with postnatal onset. [75%]
 
Cleft lip and/or cleft palate. [15%]
 
Tracheoesophageal fistula. [15%]
 
Distinctive CHARGE facial appearance, consisting of a prominent forehead and a prominent nasal bridge. [75%]
 
Other, less frequent manifestations include kidney malformations [25%], immunodeficiency, various limb abnormalities, scoliosis, dental problems, omphalocele, brain malformations, attention deficit hyperactivity disorder (ADHD), and various behavioral problems.
 
The diagnosis of CHARGE syndrome is primarily clinical, based on the use of the diagnostic criteria above.
 
External ear anomalies, abnormalities of cranial nerve function, semicircular canal hypoplasia and gross motor delays seem to be consistent phenotypic manifestations in CHARGE syndrome, but fully one third of CHARGE patients will lack choanal atresia and/or ocular colobomata, with the most mildly affected showing only abnormal ears and a balance disturbance. Consequently, CHARGE syndrome can closely resemble several other genetic and teratogenic conditions, such as the 22q11.2 deletion syndrome, Kallmann syndrome, VACTERL association, Kabuki syndrome, renal coloboma syndrome, Cat eye syndrome, Joubert syndrome, Branchiootorenal syndrome, and retinoic embryopathy. In one patient with velo-cardio-facial syndrome in whom the chromosome 22q11.2 microdeletion was ruled out, a CHD7 mutation was documented. Several patients with Kallmann syndrome were found to have CHD7 mutations.
 
In recognition of this expanding CHARGE phenotype, Bergman et al. have proposed a revision of cardinal and supporting features and suggest that CHD7 testing be offered to individuals on the milder end of the phenotypic spectrum (Bergman, 2011). Their algorithmic approach to diagnosis also incorporates temporal bone CT scans as an important but not invariantly necessary component of the diagnostic workup.
 
Genetics of CHARGE Syndrome
In 2004, mutations of CHD7, which encodes chromodomain helicase DNA-binding protein, were found to cause CHARGE syndrome. In mouse models, the CHD7 gene has been found to be associated with neural crest migration (Schulz, 2014).  Almost all pathogenic mutations have proven to be point mutations, though on rare occasions there may be a chromosomal translocation with a breakpoint within the CHD7 gene.
 
Microdeletions, as would be detected with chromosome microarray testing, are rare and probably occur in no more than 2% of individuals.
 
Most instances of CHARGE syndrome are sporadic events in a family and appear to be caused by de novo CHD7 mutations. On rare occasions CHARGE can be inherited as an autosomal dominant condition. Individuals with CHARGE who reproduce have a 50% chance of transmitting the mutation to their offspring. Recurrence in siblings because of germline mosaicism has also been reported. The prevalence of CHARGE syndrome is estimated at 1 in 8500 live births
 
Genetic testing for mutations of CHD7 is commercially available from several commercial laboratories and is generally performed through Sanger sequence analysis.
 
Treatment of CHARGE Syndrome
Extensive management guidelines have been developed for CHARGE syndrome. These include periodic examinations and treatment by ophthalmology, otolaryngology, audiology, occupational therapy, speech therapy, gastroenterology, endocrinology, cardiology, neurology, developmental pediatrics, and genetics. Routine investigations would include choanal CT, nasal endoscopy, brainstem auditory evoked responses, temporal bone CT, swallowing studies, renal ultrasound, gonadotropin testing, echocardiography, brain magnetic resonance imaging (MRI), growth hormone testing, and genetic counseling. Immunological assessment should be considered, particularly if patients have recurrent lung or ear infections (Hsu, 2014).  Many of these resources might be provided in due course for a child with multiple congenital anomalies in the absence of an exact etiologic diagnosis. However, a number of specific investigations and therapies might not be considered unless CHARGE syndrome was definitively diagnosed on a clinical basis, or, for mildly affected individuals, as the result of genetic testing.
  
Regulatory Status
No U.S. Food and Drug Administration (FDA)-cleared genotyping tests were found. Thus, genotyping is offered as a laboratory-developed test. Clinical laboratories may develop and validate tests in-house (“home-brew”) and market them as a laboratory service; such tests must meet the general regulatory standards of the Clinical Laboratory Improvement Act (CLIA).
 
Coding
CPT code 81407 includes the following testing for CHARGE syndrome:
 
CHD7 (chromodomain helicase DNA binding protein 7) (e.g., CHARGE syndrome), full gene sequence
 

Policy/
Coverage:
Meets Primary Coverage Criteria Or Is Covered For Contracts Without Primary Coverage Criteria
 
Genetic testing for CHARGE syndrome meets member benefit certificate primary coverage criteria that there be scientific evidence of effectiveness in improving health outcomes to confirm a diagnosis in a patient with signs/symptoms of CHARGE syndrome when a definitive diagnosis cannot be made with clinical criteria.  
 
Does Not Meet Primary Coverage Criteria Or Is Investigational For Contracts Without Primary Coverage Criteria
 
Mutation testing for CHARGE syndrome in all other situations does not meet member benefit certificate primary coverage criteria that there be scientific evidence in improving health outcomes.
 
For members with contracts without primary coverage criteria, mutation testing for CHARGE syndrome is considered investigational in all other situations. Investigational services are specific contract exclusions in most member benefit certificates of coverage.
 
 

Rationale:
This policy was created in 2013 and is based on a search of the MEDLINE database through June 2013. Literature that describes the analytic validity, clinical validity, and clinical utility of testing for CHARGE syndrome was sought.
 
Analytic validity (the technical accuracy of the test in detecting a mutation that is present or in excluding a mutation that is absent)
 
Almost all pathogenic mutations are point mutations. On rare occasions there may be a chromosomal translocation with a break point within the CDH7 gene. Microdeletions or whole-exon deletions occur in <5% of patients.
 
Sequencing of the CHD7 gene has high analytical sensitivity and specificity. Sequence analysis detects >996) % of the (point) mutations present in the area that has been investigated. Testing that identifies deletions not readily detected by sequence analysis includes MLPA or chromosomal microarray analysis. MLPA has an estimated sensitivity of >95% for deletions and >90% for individual exons (Blake, 2011) .
 
The analytical sensitivity (proportion of positive tests if the genotype is present) depends on the method used. If only CHD7 sequencing is performed, deletions are missed less than 5% due to whole-exon or whole-gene deletions. If sequencing is combined with MLPA, it is 100% (Blake, 2011).  
 
The analytical specificity (proportion of negative tests if the genotype is not present) is almost 100% (some variants may erroneously be interpreted as pathogenic) (Blake, 2011).
 
Clinical validity (the diagnostic performance of the test [sensitivity, specificity, positive and negative predictive values] in detecting clinical disease)
 
Clinical sensitivity and specificity are also high.
 
The clinical sensitivity (proportion of positive tests if the disease is present) can be dependent on variable factors such as age or family history, and may depend on the clinical criteria used. In over 95% of the patients who fulfil the Blake or Verloes criteria, a mutation is found (Blake, 2011). In those with suspected CHARGE syndrome, a mutation is found in 60–70% of patients.
 
CHARGE syndrome sometimes can be excluded if a patient does not fulfill the clinical criteria and does not carry a mutation or deletion of CHD7. Some conditions that mimic CHARGE syndrome are 22q11 deletion syndrome, VACTERL association, chromosomal disorders (e.g., deletions 3p12p21.2) disorders caused by teratogens (e.g., maternal diabetes, Accutane), and Kallmann syndrome (Bake, 2011).  
 
The clinical specificity (proportion of negative tests if the disease is not present) can be dependent on variable factors such as age or family history. The clinical variability of CHARGE syndrome is considerable. If the diagnosis is based on the Blake or Verloes criteria, some individuals with CHARGE will be missed. The clinical specificity is greater than 95%, since less than 5% of the patients with a CHD7 mutation do not completely fulfill these criteria. However, it should be taken into account that the mild end of the phenotypic spectrum is not completely known yet (Blake, 2011).
 
Therefore, genetic testing for CHARGE syndrome is very good for confirming a diagnosis, but a negative test does not rule out the disease.
 
The positive clinical predictive value (life-time risk to develop the disease if the test is positive) is 100%, but there is high clinical variability.
 
The negative clinical predictive value (probability of not developing the disease if the test is negative), assuming an increased risk based on family history, is 100% if the index case in the family has been tested. If the index case in the family has not been tested, it depends on the a priori chance of the index to find a mutation, which is 60-90%. Complete analysis (sequencing and MLPA) will reduce this by 90-95%.
 
There are no known genotype-phenotype correlations for specific CHD7 mutations and CHARGE syndrome manifestations, and therefore, the phenotype cannot be predicted from the genotype. Clinical utility (how the results of the diagnostic test will be used to change management of the patient and whether these changes in management lead to clinically important improvements in health outcomes)
 
Individual
Most cases of CHARGE syndrome can be diagnosed clinically using established major and minor criteria. Scanning of the temporal bones often elicits abnormalities in the semi-circular canals, which brings more specificity to the diagnosis.
 
However, not all patients fulfill the clinical criteria for CHARGE syndrome, and based on clinical findings, may be considered to have possible or probable CHARGE syndrome. Mildly affected patients may only have one or a few of the features of CHARGE syndrome. Overlapping features with other syndromes may also make a clinical diagnosis challenging.
 
Genetic testing may be useful in patients who do not have the classical CHARGE characteristics and may be at risk for the long-term complications of CHARGE syndrome (Blake, 2011).
 
Extensive management guidelines have been developed for CHARGE syndrome. These include periodic examinations and treatment by ophthalmology, otolaryngology, audiology, occupational therapy, speech therapy, gastroenterology, endocrinology, cardiology, neurology, developmental pediatrics, and genetics. Routine investigations would include choanal CT, nasal endoscopy, brainstem auditory evoked responses, temporal bone CT, swallowing studies, renal ultrasound, gonadotropin testing, echocardiography, brain MRI, growth hormone testing, and genetic counseling.
 
Relatives
 
Almost all patients diagnosed with CHARGE syndrome do not have an affected parent as most are de novo mutations. Only rare instances of transmission from a mildly affected parent have been reported (Sanlaville, 2007). Therefore, genetic testing in relatives of a patient with CHARGE syndrome has low clinical utility.
 
Preconception (carrier) testing and prenatal (in utero) testing can also be performed, but are not addressed in this literature review.
 
Summary
CHARGE syndrome is a rare genetic syndrome with multiple associated malformations. Established clinical criteria can provide a diagnosis of definite CHARGE syndrome in some patients, however, due to the variable phenotypes associated with CHARGE syndrome, some patients may be categorized clinically as having possible or probable CHARGE syndrome.
 
CDH7 is the only gene currently known to be associated with CHARGE syndrome. The analytic sensitivity and specificity for detecting mutations in the CHD7 gene is high. The clinical sensitivity and specificity are also high: among patients with a clinical diagnosis of definite CHARGE syndrome, 90-95% have a mutation of CHD7. For individuals with possible or probable CHARGE syndrome, CHD7 analysis is positive for a mutation in 65-70% of cases.
 
The clinical utility of making a definite diagnosis of CHARGE syndrome is high, in that confirming a diagnosis in a patient will lead to changes in clinical management, including clinical assessment and treatment recommendations that are well-defined. The clinical utility of genetic testing for CHARGE syndrome is for patients in whom a definite diagnosis cannot be made clinically. Therefore, genetic testing for CHARGE syndrome may be considered medically necessary to confirm a diagnosis in a patient with signs/symptoms of CHARGE syndrome when a definitive diagnosis cannot be made with clinical criteria.
 
Almost all cases of CHARGE syndrome are a result of a de novo mutation, and therefore testing of relatives of a patient with CHARGE syndrome has low clinical utility. Therefore, mutation testing for CHARGE syndrome is considered investigational in all other situations.
 
Practice Guidelines and Position Statements
Bergman et al have proposed guidelines for CDH7 analysis, and state that while the diagnosis of CHARGE syndrome remains primarily a clinical diagnosis, molecular testing can confirm the diagnosis in mildly affected patients (Bergman, 2011).
 
2015 Update
A literature search conducted through May 2015 did not reveal any new information that would prompt a change in the coverage statement. The key identified literature is summarized below.
 
 
Analytic Validity
(technical accuracy of the test in detecting a mutation that is present or in excluding a mutation that is absent)
 
Almost all pathogenic mutations are point mutations. More than 500 specific CDH7 mutations associated with CHARGE syndrome have been identified (Kim, 2014). On rare occasions, there may be a chromosomal translocation with a break point within the CDH7 gene. Microdeletions or whole-exon deletions occur in less than 5% of patients.
 
Ongoing Clinical Trials
A search of the online site ClinicalTrials.gov in March 2015 found no ongoing trial addressing the use of genetic testing for CHARGE syndrome.
 
Summary
CHARGE syndrome is a rare genetic condition associated with multiple congenital anomalies. In many individuals, the diagnosis can be made based on clinical findings. However, the phenotype of the disease is highly variable, and some patients do not fulfill the criteria for a definite diagnosis by clinical findings. Sequence analysis of the chromodomain helicase DNA binding protein 7 (CHD7) coding region detects mutations in most individuals with CHARGE syndrome.
  
2016 Update
A literature search conducted through May 2016 did not reveal any new information that would prompt a change in the coverage statement.
 
2017 Update
A literature search conducted through May 2017 did not reveal any new information that would prompt a change in the coverage statement. The key identified literature is summarized below.
 
Analytic Validity
Analytic validity is the technical accuracy of a test in detecting a variant that is present or in excluding a variant that is absent.
 
Almost all pathogenic variants are single-nucleotide variants (SNVs). More than 500 specific CHD7 variants associated with CHARGE syndrome have been identified (Kim, 2014; Janssen, 2012). On rare occasions, there may be a chromosomal translocation with a break point within the CHD7 gene. Microdeletions or whole-exon deletions occur in less than 5% of patients.
 
Clinical Validity
Clinical validity is the diagnostic performance of a test (sensitivity, specificity, positive and negative predictive values) in detecting clinical disease.
 
The yield of genetic testing in individuals with either diagnosed or suspected CHARGE syndrome can vary depending on factors such as age or family history, and may depend on the clinical criteria used. As reported in the Clinical Utility Gene Card (2015), in over 90% of the patients who fulfill the Blake or Verloes criteria, a disease-associated variant is found (van Ravenswaaij, 2015).
 
In those with suspected CHARGE syndrome, a disease-associated variant is found in 30% to 60% of patients. The proportion varies in individual studies, especially those with small sample sizes. For example, in 2006, Lalani and colleagues conducted genetic testing in 110 individuals with a clinical diagnosis of CHARGE syndrome and found disease-associated variants in CHD7 in 64 (58%) of study participants (Lalani, 2006).
 
2018 Update
A literature search conducted using the MEDLINE database through May 2018 did not reveal any new information that would prompt a change in the coverage statement.

CPT/HCPCS:
81407MOLECULAR PATHOLOGY PROCEDURE LEVEL 8

References: Bergman JE, Janssen N, Hoefsloot LH et al.(2011) CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype. J Med Genet 2011; 48(5):334-42.

Blake K, van Ravenswaaij-Arts CM, Hoefsloot L et al.(2011) Clinical utility gene card for: CHARGE syndrome. Eur J Hum Genet 2011; 19(9).

Blake KD, Davenport SL, Hall BD et al.(1998) CHARGE association: an update and review for the primary pediatrician. Clin Pediatr (Phila) 1998; 37(3):159-73.

Hsu P, Ma A, Wilson M, et al.(2004) CHARGE syndrome: A review. J Paediatr Child Health. Feb 19 2014. PMID 24548020

Hughes SS, Welsh HI, Safina NP, et al.(2014) Family history and clefting as major criteria for CHARGE syndrome. Am J Med Genet A. Jan 2014;164A(1):48-53. PMID 24214489

Issekutz KA, Graham JM, Jr., Prasad C et al.(2005) An epidemiological analysis of CHARGE syndrome: preliminary results from a Canadian study. Am J Med Genet A 2005; 133A(3):309-17.

Jain S, Kim HG, Lacbawan F, et al.(2011) Unique phenotype in a patient with CHARGE syndrome. Int J Pediatr Endocrinol. Oct 13 2011;2011:11. PMID 21995344

Janssen N, Bergman JE, Swertz MA, et al.(2012) Mutation update on the CHD7 gene involved in CHARGE syndrome. Hum Mutat. Aug 2012;33(8):1149-1160. PMID 22461308

Kim Y, Lee HS, Yu JS, et al.(2014) Identification of a novel mutation in the CHD7 gene in a patient with CHARGE syndrome. Korean J Pediatr. Jan 2014;57(1):46-49. PMID 24578717

Lalani SR, Hefner MA, Belmont JW et al.(2012) CHARGE Syndrome. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong CT, Stephens K, et al., editors. GeneReviews™ [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2013. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1117/.

Lalani SR, Hefner MA, Belmont JW.(2017) GeneReviews: CHARGE syndrome. 2012; https://www.ncbi.nlm.nih.gov/books/NBK1117

Lalani SR, Safiullah AM, Fernbach SD, et al.(2006) Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation. Am J Hum Genet. Feb 2006;78(2):303-314. PMID 16400610

Sanlaville D, Verloes A.(2007) CHARGE syndrome: an update. Eur J Hum Genet 2007; 15(4):389-99.

Schulz Y, Wehner P, Opitz L, et al.(2014) CHD7, the gene mutated in CHARGE syndrome, regulates genes involved in neural crest cell guidance. Hum Genet. Apr 13 2014. PMID 24728844

Tellier AL, Cormier-Daire V, Abadie V et al.(1998) CHARGE syndrome: report of 47 cases and review. Am J Med Genet 1998; 76(5):402-9.

van Ravenswaaij-Arts CM, Blake K, Hoefsloot L, et al.(2015) Clinical utility gene card for: CHARGE syndrome - update 2015. Eur J Hum Genet. Nov 2015;23(11). PMID 25689928


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