Genetic testing in ectodermal dysplasia: Availability, clinical utility, and the nuts and bolts of ordering a genetic test†
How to cite this article: Bale SJ, Mitchell AG. 2009. Genetic testing in ectodermal dysplasia: Availability, clinical utility, and the nuts and bolts of ordering a genetic test. Am J Med Genet Part A 149A:2052–2056.
“Ectodermal Dysplasia syndromes” comprise a diverse group of heritable conditions characterized by congenital anomalies of one or more ectodermal structures and their appendages: hair, teeth, nails, and sweat glands. Genetic testing is available for many types of ectodermal dysplasia (ED) through clinical and/or research laboratories. We address the distinctions between genetic testing as performed on a clinical versus research basis, and summarize the clinical aspects, testing methodology, and sensitivity for those ED syndromes for which testing is available in a clinical laboratory. Lastly, we leave the laboratory for the clinical setting to discuss the utility of genetic testing for patients and their families, and summarize the practical issues involved in ordering a genetic test. © 2009 Wiley-Liss, Inc.
Availability of genetic testing for ectodermal dysplasia (ED) syndromes has expanded rapidly in recent years. While clinical laboratories offer diagnostic testing for the more common of the ED syndromes, genetic testing for the rarer ED conditions is performed exclusively on a research basis. For some ED syndromes, both types of analyses are available. In an effort to differentiate these genetic testing options, we discuss the significant contrasts between clinical and research testing, and list the current availability of clinical and/or research testing for each ED condition.
The ED syndromes comprise a large and diverse group of congenital heritable conditions characterized by the involvement of one or more ectodermal structures and their appendages: hair, teeth, nails, and sweat glands. For those ED disorders with clinically available genetic testing, a brief summary of the clinical findings, inheritance pattern, testing methodology, and sensitivity is presented.
Perhaps the largest consideration when weighing the decision to have or decline genetic testing is its clinical utility. We examine this complex topic as it pertains to a patient's medical care, the family, and prenatal diagnosis. Additionally, we review the practical issues of how to identify a laboratory that performs a particular test, the necessary steps to obtain a genetic test, sample requirements, and payment issues.
CLINICAL TESTING VERSUS RESEARCH TESTING
Clinical genetic testing in the United States is performed only in CLIA-certified diagnostic laboratories. The Clinical Laboratory Improvement Amendments (CLIA) Act was first passed in 1988 to assure high quality laboratory testing by setting minimum standards for all laboratories to follow and providing for on-site inspections to determine if laboratories are achieving those standards. Current CLIA oversight is managed by The Centers for Medicare and Medicaid Services (CMS) which regulates all laboratory testing (except research) performed on humans in the United States. CLIA standards apply to any laboratory result that will be used for diagnosis, treatment, or management of a patient. Genetic testing done in a clinical laboratory incurs a fee for the patient, institution, or insurance company. The cost of a genetic test may range from $100 to over $6,000 depending on the size of the gene to be evaluated and complexity of the testing methodology utilized. If a third-party payer (e.g., Medicare, Medicaid, commercial insurance) is being requested to cover the costs of the testing, they generally require that a laboratory is CLIA-certified. Published turn-around times for when results can be expected to be completed are made available by most commercial laboratories through their websites or printed materials. The physician or other health care practitioner ordering the genetic test receives a written report of the test results, including an interpretation and recommendations for appropriate follow-up.
In contrast, research genetic testing is usually performed in academic settings, in laboratories that are not certified under the CLIA regulation. Thus, although the testing may be of high quality, there is no requirement that the safeguards outlined in the CLIA regulation are followed. It is the spirit of the CLIA regulation that results of genetic testing produced in a research laboratory are not to be released to the referring physician to be placed in patient records for use in the diagnosis, therapy, or management of a patient, and the research laboratory is technically in violation of the federal law every time it issues a test result [Grody and Richards, 2008]. Turn-around times may be long (months to years, in many cases) and generally neither the participating patient nor the physician who may have referred the patient to the study will receive a written report of the patient's genetic test results, although a summary of study results for all participating patients may be released. As opposed to the clinical laboratory, where the main purpose is to provide specific information to a particular patient in a timely manner, to be used for diagnosis, management, treatment, and family planning decisions, the underpinning of research testing is advancement of the understanding of the genetic condition by, among other pursuits, identifying unknown genes or uncovering information about the function of the gene at a cellular or organism level. Therefore, because the primary focus of a research institution is not to furnish diagnostic test results for a specific individual, individuals who voluntarily participate in the studies typically are not charged a testing fee.
LIST OF ED SYNDROMES FOR WHICH GENETIC TESTING IS CURRENTLY AVAILABLE
As of June 1, 2008, genetic testing for the following ED syndromes is available in one or more clinical laboratory [GeneTests, www.genetests.org]:
Hypohidrotic ectodermal dysplasia (HED), X-linked (EDA1 gene).
HED, autosomal (EDAR gene).
Ectrodactyly ectodermal dysplasia-clefting (EEC) syndrome and related disorders (TP73L gene).
Clouston hidrotic ectodermal dysplasia; Clouston syndrome (GJB6 gene).
HED with immune deficiency (NEMO (aka IKBKG) gene).
Focal dermal hypoplasia; Goltz syndrome (PORCN gene).
Keratitis-ichthyosis-deafness (KID) syndrome (GJB2 gene).
Fraser syndrome (FRAS1 and FREM2 genes).1
As of June 1, 2008, genetic testing for the following ED syndromes is available exclusively on a research basis [GeneTests, www.genetests.org]:
Ellis-van Creveld syndrome (EVC gene).
Ectodermal dysplasia, ectrodactyly, and macular dystrophy; EEM syndrome (CDH3 gene).
As of June 1, 2008, genetic testing for the following ED syndromes is available in both clinical and research settings [GeneTests, www.genetests.org]:
HYPOHIDROTIC ECTODERMAL DYSPLASIA, X-LINKED AND AUTOSOMAL
The clinical presentation of HED includes fine, sparse and light-colored scalp and body hair (hypotrichosis), decreased ability to sweat leading to heat intolerance, and missing, conical or peg shaped teeth. The facial features are characterized by periorbital hyperpigmentation, saddle nose, and full lips. In the X-linked form, female carriers may have minor symptoms features, such as thin hair, patches of hypohidrosis, and abnormal teeth or occasionally, may exhibit full features of the syndrome. In the autosomal form of HED, males and females are affected equally.
Mutation in the EDA1 gene is associated with the X-linked form of HED, and can be identified in 75–95% of patients with a positive family history consistent with X-linkage, and in about half of sporadic cases (no family history). Thus, bi-directional full gene sequencing of EDA1 is recommended in both males and females who present with HED. Partial or whole deletions of EDA1 account for fewer than 10% of mutations in the gene. Hemizygous deletions in males are readily identified by failure to amplify one or more exons of the gene using the polymerase chain reaction (PCR). Quantitative PCR is needed for detection of heterozygous EDA1 deletions in females in most instances. If no pathogenic mutation is identified on analysis of the EDA1 gene, full sequencing of the EDAR gene is available and can be considered, particularly in patients with no family history of ED, or in which X-linked inheritance is excluded due to male-to-male transmission. Although mutations in EDAR account for less than 5% of HED, it is responsible for both autosomal dominant and autosomal recessive forms, complicating interpretation and estimation of recurrence risk [Monreal et al., 1998, 1999; Chassaing et al., 2006].
ECTRODACTYLY-ECTODERMAL DYSPLASIA-CLEFTING (EEC) SYNDROME AND RELATED DISORDERS
Autosomal dominant EEC syndrome is characterized by limb malformations (ectrodactyly is present in 2/3 of patients, while other findings include split hand-split foot malformation and polysyndactyly), ED (hypohidrosis, hypotrichosis, and anodontia), and cleft lip and palate (in 40% of patients; isolated cleft lip or palate is rare). Associated findings may include lacrimal-duct abnormalities, urinary tract anomalies, minor facial anomalies, and developmental delay.
Approximately 98% of patients with the classic EEC phenotype have mutations in the TP73L gene (the gene is alternately known at TP63), specifically in exons 5–8, 13, and 14. Standard testing includes bi-directional sequencing of these exons where most mutations are located. If no mutation is detected in these six exons, sequencing of the remainder of the TP73L gene is also available. Mutations are almost exclusively missense changes that cluster in the DNA binding domain of the protein. Five “hot spot” mutations have been found in ∼87% of all patients [Rinne et al., 2006].
Allelic disorders also associated with TP73L mutations include Limb–Mammary syndrome (LMS), ADULT syndrome, Hay-Wells syndrome (HWS; also know as Ankyloblepharon-Ectodermal Defects-Cleft lip/palate syndrome or AEC), Rapp Hodgkin syndrome (RHS), and Split Hand-Split Foot Malformation (SHFM).
CLOUSTON HIDROTIC ECTODERMAL DYSPLASIA; CLOUSTON SYNDROME
In contrast to the more common X-linked form of ED, most patients with autosomal dominant Clouston Hidrotic Ectodermal Dysplasia have normal sweat and sebaceous gland function, partial to total alopecia, nail hypoplasia and deformitiy, skin hyperpigmentation particularly over the joints, normal teeth, and palmoplantar keratoderma.
Bi-directional sequencing of exon 3, the single coding exon of the GJB6 gene, is expected to identify nearly 100% of mutations in clinically diagnosed individuals. There are two common missense mutations in the GJB6 gene, G11R, and A88V. G11R is the cause of Clouston Hidrotic ED in all French-Canadians families tested to date, while the A88V mutation has been described in patients from India, Malaysia, and Wales. At least three families diagnosed with pachyonychia congenita and without keratin gene mutations were found to harbor G11R or A88V mutations in GJB6. A third mutation, V37E, has been associated with two ED disorders with overlapping features: Clouston syndrome and KID syndrome with congenital atrichia. For patients with suspected Clouston syndrome who do not harbor a mutation in GJB6, sequence analysis of the GJB2 gene associated with KID syndrome may be considered [Lamartine et al., 2000; van Steensel et al., 2003; Jan et al., 2004].
HYPOHIDROTIC ECTODERMAL DYSPLASIA WITH IMMUNE DEFICIENCY (HED-ID)
This X-linked recessive disorder is characterized in affected males by HED in combination with recurrent infections of the digestive tract, respiratory tract, and skin. Bi-directional sequence analysis of the coding region and splice junctions of the IKBKG (NEMO) gene (exons 1–10) is available for diagnosis. Based on a small number of studies, the detection rate approaches 100% in clinically affected individuals [Zonana et al., 2000; Döffinger et al., 2001]. Also due to mutations in the IKBKG gene is the allelic disorder Incontinentia Pigmenti (IP) which follows an X-linked pattern of inheritance, with lethality in males.
FOCAL DERMAL HYPOPLASIA; GOLTZ SYNDROME
Focal dermal hypoplasia, or Goltz syndrome, is a multisystem disease caused by developmental abnormalities in the meso- and ectoderm. Affected individuals have clinical manifestations involving the skin (focal hypoplasia/atrophy of skin with herniation of fat into the dermal layer and pigmentary abnormalities), hair (sparse, patchy, brittle), teeth (hypo/oligodontia, enamel hypoplasia/pitting, abnormal shape), nails (dystrophic/absent), and eyes (coloboma, micro/anophthalmia, aniridia). In addition to the ectodermal component, limb and digital anomalies, short stature, breast anomalies, and facial anomalies may be present. Approximately 15% of affected individuals have mental retardation.
This disorder follows X-linked dominant inheritance with 90% of the cases being female. Mutations in 95% of females and all males arise de novo [Goltz, 1992]. Affected males, and some females, are mosaic and have a milder disease course.
Comprehensive genetic testing requires both sequence analysis and deletion studies as ∼17% of cases are due to a complete deletion of the PORCN gene. [Grzeschik et al., 2007; Wang et al., 2007; Leoyklang et al., 2008]. This dual testing strategy is expected to identify pathogenic mutations (including deletions) in approximately 2/3 of clinically diagnosed individuals. Patients with a very low level of mosaicism for PORCN mutations are more difficult to identify, and analysis of DNA derived from more than one tissue may be necessary (e.g., blood and cultured fibroblasts).
KERATITIS-ICHTHYOSIS-DEAFNESS (KID) SYNDROME
KID syndrome is a rare and phenotypically variable etodermal dysplasia affecting the skin, hearing, and vision. Usually manifesting at birth or during infancy, this disorder is characterized by thickening of the skin (hyperkeratosis) with redness (erythrokeratoderma), including palms and soles (palmoplantar keratoderma). Other manifestations include chronic inflammation of the lips (cheilitis), increased susceptibility to skin infections, nail dystrophy, scarring alopecia, dental anomalies, heat intolerance and, less commonly, squamous cell carcinoma. Eye manifestations include photophobia, progressive clouding of the cornea (keratitis) and corneal neovascularization, which may eventually lead to decline of vision or blindness. Sensorineural hearing loss is often congenital, bilateral and severe.
While KID syndrome is inherited in an autosomal dominant fashion, over 90% of cases arise from a de novo mutation. Bi-directional sequencing of the single coding exon 2 of the GJB2 gene identifies the disease-causing mutation in most patients [Richard et al., 2002]. Although mutations can occur throughout the exon, a single mutation, G50N, accounts for many of the cases. Rarely, patients with KID syndrome and congenital atrichia have been reported to harbor mutations in the GJB6 gene [Jan et al., 2004].
CLINICAL UTILITY OF GENETIC TESTING FOR ED SYNDROMES
When a patient presents with a suspected diagnosis of an ED syndrome for which genetic testing is available, the situation may appear clear-cut and ideal for clinicians to offer mutation analysis and for patients to consent. Deeper consideration of the test's clinical utility, however, can guide discussions between patients and providers regarding whether genetic testing results are a necessary component to providing optimal management of the patient and family, and represents a requisite step in the genetic counseling process.
For children with classical manifestations of a particular ED syndrome and consistent inheritance pattern in the family such that a reliable diagnosis can be made without further testing, medical management of the patient will not be dependant on the result obtained by genetic testing. On the other hand, there are reasons for utilizing genetic testing to confirm a patient's clinical diagnosis. For example, when a patient presents with mild or atypical ED such that a diagnosis cannot be made by clinical findings alone, genetic testing may allow for a definitive diagnosis to be established. A definitive diagnosis can help a patient and his/her family have a better understanding of what to expect in the future. Knowledge of the natural history and prognosis of the ED can help families anticipate future expenses, issues related to home, school, or work, and provide support for their efforts to obtain resources to address anticipated school, medical, and financial issues that may arise in the future.
In patients with HED and no relevant family history to differentiate between X-linked and autosomal forms of the disease, testing of the EDA1 and EDAR genes to determine underlying cause and infer inheritance pattern will provide the information necessary to offer unaffected, but at-risk, family members testing to determine carrier status. Carrier testing is particularly relevant to families in which either EDA1 or EDAR mutations are segregating with HED.
For some couples who are at risk of having a child with an ED syndrome, knowledge of the specific mutation underlying the disorder in their family is requisite to offering prenatal testing in future pregnancies. In fact, it is because of an interest in prenatal diagnosis that most individuals will request genetic testing for mutation identification in the affected individual in their family. Once the mutation is identified, family planning options, including early prenatal diagnosis, in vitro fertilization followed by preimplantation genetic diagnosis, and other assisted reproductive technologies becomes available.
Genetic testing is also relevant to the patient if the result has currently, or may in the future, have a clear clinical application such as a specific therapy, where knowledge of the underlying faulty gene in a patient will be required for gene-based therapies.
NUTS AND BOLTS OF HOW TO ORDER A GENETIC TEST
The first step in ordering a genetic test is to identify the laboratory or laboratories that offer testing. While the technologies utilized for genetic testing in the EDs are similar across laboratories, the analysis and result interpretation is often complex. There is a highly useful, on-line resource, to assist medical professionals in identifying laboratories offering testing for any particular gene. www.genetests.org allows one to search by disease or gene to find a laboratory that provides testing, a description of test methodology, and laboratory contact information for additional questions.
The second step is to determine who in the family to test. Genetic disease often affects a whole family rather than just one individual. Still, genetic testing has to start with someone. It is recommended to first test a family member who is affected with the genetic disorder, as this person has a higher chance of having a disease-associated mutation than an unaffected relative. If a mutation is identified in an affected individual, then other at-risk relatives can be tested. This testing strategy will provide the most accurate result for the family and is most cost-effective. If testing for a specific genetic disorder is not currently available, consider banking the DNA of an affected individual for testing in the future when it becomes available.
It is important to be aware of the turn-around time (TAT) for when test results are expected to be complete. In a clinical laboratory, the TAT for genetic results can be measured in weeks to months. Most clinical laboratories publish testing TAT on their websites or can give you this information over the phone. Understanding the TAT can help clinicians and genetic counselors manage patient expectations about when they will have their “news,” and help patients to plan ahead when prenatal diagnosis is desired.
A laboratory may have a specific preference for the type of specimen submitted for analysis. Specifications can be found on most laboratory websites or by contacting the laboratory directly. For diagnostic purposes, most laboratories require a blood specimen, usually whole blood in EDTA or another anticoagulant. Some laboratories may accept buccal specimens. For prenatal testing, it is important to contact the laboratory directly regarding sample type (chorionic villi or amniocytes, either fresh or cultured, etc.) and any other samples from other family members that may be required for completion and interpretation of test results. In some cases, both the maternal and paternal samples will be required. In nearly all situations, the laboratory will require that the proband's mutation is identified, and may also need to be confirmed independently by the laboratory doing the prenatal test.
Of concern to the family will be an understanding of the payment options. Genetic testing is often expensive. Insurance generally pays a portion of the total cost, but beware that some insurers and Medicare do not cover the cost of any genetic testing. It is essential to obtain pre-authorization from the insurer (preferably in writing) prior to ordering the test and sending the sample to the laboratory. Working with a genetic counselor can also greatly aid in obtaining testing coverage. He/she can write a letter of medical necessity to the insurer that explains the indications for testing, and help with gathering ICD (diagnosis codes) and CPT (procedure codes) required by the insurance company to evaluate and approve the request for genetic testing services.
Finally, it is always helpful to work with a genetic counselor when considering genetic testing for a patient or family. Genetic counselors and other genetics specialists are trained to educate and assist patients in understanding the risks and benefits associated with testing, and in interpreting the results to the patient, and explaining the options available to family members based on knowledge of genetic testing results. To locate a genetic specialist, visit the membership directory of the American College of Medical Genetics (www.acmg.net) or the National Society of Genetic Counselors (www.nsgc.org).
Per GeneTests.org, mutation analysis of exon 6 of the FREM2 gene associated with Fraser syndrome is available in a CLIA-certified laboratory in Portugal, however the availability of this test could not be confirmed.