The Journal of Molecular Diagnostics, Vol. 13, No. 1, January 2011 Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved. DOI: 10.1016/j.jmoldx.2010.11.012
Special Article Population Carrier Screening for Spinal Muscular Atrophy A Position Statement of the Association for Molecular Pathology
Kasinathan Muralidharan,*† Robert B. Wilson,*‡ Shuji Ogino,*§ Narasimhan Nagan,*¶ Christine Curtis,*储 and Iris Schrijver*,** From the Clinical Practice Committee of the Association for Molecular Pathology (AMP)* and Quest Diagnostics Nichols Institute,† Chantilly, Virginia; the Department of Pathology and Laboratory Medicine,‡ University of Pennsylvania, Philadelphia, Pennsylvania; the Department of Pathology,§ Brigham and Women’s Hospital, Boston, Massachusetts; the Molecular Diagnostics Laboratory,¶ Genzyme Corporation, Westborough, Massachusetts; the Center for Human Genetics Laboratory,储 University Hospitals-Case Medical Center, Case Western Reserve University, Cleveland, Ohio; and the Departments of Pathology and Pediatrics,ⴱⴱ Stanford University School of Medicine, Stanford, California. From the SMA Position Statement Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee
Spinal muscular atrophy is a common and often fatal autosomal recessive disorder for which carrier screening is available. The Association for Molecular Pathology has evaluated recent opinions regarding population carrier screening, reviewed the current literature, and developed a position statement that includes specific recommendations addressing both diagnostic and practical issues that affect implementation. ( J Mol Diagn 2011, 13: 3– 6; DOI: 10.1016/j.jmoldx.2010.11.012)
Spinal muscular atrophy (SMA, MIM#253300) is the second most common fatal autosomal recessive disorder after cystic fibrosis, affecting approximately 1 in 6000 to 10,000 live births.1,2 It is characterized by hypotonia, proximal muscle weakness, and respiratory distress due to degeneration of motor neurons in the spinal cord. The clinical presentation of SMA is highly variable, ranging in onset from infancy to adulthood and in severity from profound hypotonia to minor muscle weakness. SMA has been classified into four groups based on age
of onset and motor function achieved.3 Type I SMA with onset of disease symptoms before 6 months of age and death from respiratory failure within 2 years of life accounts for 60% to 70% of SMA. Type II SMA, which is characterized by onset of symptoms after 6 months of age, significant respiratory distress, an inability to stand or walk unaided, and a variable lifespan, accounts for 20% to 30% of SMA. Types III and IV are milder forms of SMA with onset of disease during infancy or youth and a retained ambulatory capacity. These two types account for the remaining 10% to 20% of SMA.4,5 SMA is caused by mutations in the survival motor neuron 1 (SMN1) gene (Entrez Gene ID number 6606). A homologous pseudogene of SMN1, called SMN2, lies in an inverted orientation in cis- with SMN1 on chromosome 5q11-q13. Variations in the number of copies of SMN1 and SMN2 are common. SMN1 and SMN2 differ by just five nucleotides, only one of which, in exon 7, is within the coding region. This sequence change affects splicing and results in much reduced expression levels of fulllength, functional protein from the SMN2 gene. The loss of both functional copies of the SMN1 gene, most often The 2010 AMP Clinical Practice Committee consisted of M. Fernanda Sabato Charreun, Michelle Dolan, Christine A. Curtis, William K. Funkhouser, Jane Gibson, Neal Lindeman, Ira Lubin, Federico Monzon, Narasimhan Nagan, Joseph F. Pulliam, Iris Schrijver (Chair), Patrik Vitazka, Jeffrey D. Wisotzkey, Donna M. Wolk, and Belinda Yen-Lieberman. Accepted for publication July 15, 2010. K.M. is employed by and has stock options with Quest Diagnostics. N.N. is employed by and has stock options with Genzyme Corporation. The views expressed in this article (or position statement) are expressly the opinion of the authors and do not indicate any position of their employers. Standard of practice is not being defined by this article, and there may be alternatives. Corresponding author: Iris Schrijver, M.D., Department of Pathology, L235, Stanford University Medical Center, 300 Pasteur Dr., Stanford, CA 94305. E-mail:
[email protected]. Address reprint requests to The Association for Molecular Pathology, c/o Mary Williams, 9650 Rockville Pike, Bethesda, MD 208143993. E-mail:
[email protected].
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due to deletion and/or gene conversion of SMN1 to SMN2, is the main cause of SMA. Such patients retain at least one copy of the SMN2 gene. An inverse relationship between the severity of the disease and the number of SMN2 gene copies in an affected individual has been observed.6 There are indications of other modifying factors that influence the phenotypic variability of SMA. The molecular diagnosis of SMA is accomplished through the detection of homozygous deletions of SMN1. The presence of SMN2 and the varying numbers of both SMN1 and SMN2 complicate molecular testing, but the sequence differences between the two genes allow them to be distinguished. More than 95% of SMA patients have a homozygous deletion of SMN1 exon 7. Approximately 5% of the affected patients carry other rearrangements and/or point mutations in the SMN1 gene that are not detected by the deletion assay. Because SMA is an autosomal recessive disorder, most parents are unaware of their carrier status until they have an affected child. Carrier testing of parents of affected individuals, especially those with a known genotype, has been available for more than a decade. SMA carrier testing can be performed through assessment of the SMN1 copy number. Unaffected individuals carry at least one copy of the telomeric SMN1 gene on chromosome 5 and variable copy numbers of the centromeric SMN2 gene. The complex SMN genotypes, which result from duplications and deletions of SMN1 and SMN2, have been well documented and affect the accuracy of carrier testing. The occurrence of two copies of the SMN1 gene on one chromosome 5 and zero copies on the other (the “2 ⫹ 0” genotype) is recognized as a source of false-negative carrier testing results. Since approximately 5% of normal individuals have three copies of SMN1 overall, the presence of two SMN1 copies on one chromosome 5 is far from uncommon. SMN1 point mutations are not detectable by current methods of dosage analysis and present another potential source of false-negative carrier test results.4 Finally, even for couples with one identified carrier, SMA has a relatively high de novo mutation rate,5 with de novo rearrangements found in approximately 2% of indexed patients.7 Incidence and prevalence of clinically typical SMA suggest a positive diagnosis in approximately one in every 10,000 live births and a carrier frequency of about one in 50. However, carrier testing data from more than 1200 unaffected individuals without a family history suggest a carrier frequency of approximately one in 38,8 which extrapolates to an incidence of around one in 6000 live births under Hardy-Weinberg equilibrium. There are several possible explanations for this discrepancy, including chance variation and/or embryonic lethality of some severely affected conceptuses. It has been hypothesized that an important contributor to this discrepancy may be the occurrence of clinically atypical SMA caused by homozygous deletion of the SMN1 gene.5
mending that SMA carrier testing be offered to all couples, regardless of race or ethnicity, to allow carriers to make informed reproductive choices (http://www.acmg.net/ AM/Template.cfm?Section⫽Practice_Guidelines, last accessed August 15, 2010).4 The American College of Medical Genetics contends that SMA meets the criteria for population-based carrier screening by virtue of its clinical severity and high carrier frequency, and because of the availability of reliable assays for carrier and prenatal testing. The American College of Obstetricians and Gynecologists (ACOG, now called the American Congress of Obstetricians and Gynecologists) committee on genetics published an opinion that preconception and prenatal screening for SMA in the general population is premature at this time. ACOG recommended that SMA carrier screening should be offered to patients with a family history of SMA.9 While acknowledging that SMA meets some of the common criteria for population-based screening, the ACOG asserts that specific issues remain to be addressed before implementation. These issues include the critical assessment of pilot screening studies, determination of best practices for preand posttest education and counseling, analyses of cost effectiveness, development of educational materials for patients and physicians, and laboratory standards for testing and reporting. Practice guidelines serve the purpose of bridging the gap between research and practice.10 They guide clinical practice, frequently serve as the main source of information for health care providers, patients, and other stakeholders, and influence the development and marketing of diagnostics and drugs. However, the formulation of evidence-based guidelines is complex. Apart from the critical evaluation of available information and its translation into recommendations, the creation of such guidelines requires a process in which risks and benefits, cost, and the capacity and ability of the health care system to implement the recommendations must be assessed. In disease conditions that involve different medical disciplines, it is not unusual to encounter guidelines with different positions. With collaboration, discussion, and clarification, guidelines can evolve over time and culminate in a consensus practice that balances risk, cost, and patient benefit. In the context of the differing positions of the American College of Medical Genetics and ACOG on population-based carrier screening for SMA, the Association for Molecular Pathology (AMP) has evaluated the issues and developed a position statement to include specific recommendations for population-based carrier screening for SMA.
Position Statement and Specific Recommendations Position Statement
Background to Practice Recommendations The American College of Medical Genetics has issued a practice guideline on carrier screening for SMA, recom-
AMP recognizes the utility of SMA carrier screening given the high incidence and severe nature of this condition. Furthermore, the advances in our knowledge about SMA
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and the technical developments in our ability to identify SMA carriers place us at the threshold of feasibility of population-based carrier screening for SMA. AMP recommends that implementation of SMA carrier testing be performed in a step-wise fashion and that the following critical issues be actively and expeditiously explored, pursued, and resolved before full implementation.
Specific Recommendations 1. Organize Community Involvement to Identify Issues, Set Priorities, and Develop Solutions Cystic fibrosis carrier screening is an example of recently implemented population-based carrier screening. Using this as a model, AMP recommends meetings to engage medical (clinical and laboratory) experts and other interested parties, such as parent groups, researchers, health care providers, ethicists, and payers, to identify issues, set priorities, and develop solutions. One way to facilitate such meetings would be the formation of an advisory committee on carrier screening for heritable disorders that is analogous to the Advisory Committee on Heritable Diseases in Newborns and Children for newborn screening. This will enable the development of a well-defined plan for implementation of population carrier screening for SMA. 2. Pilot Programs before General Implementation Before full implementation, SMA population-based screening pilot programs should first be offered in clearly delineated, perhaps statewide, programs. A recently published population-based SMA carrier screening pilot study demonstrated that i) the majority of patients (98.7%) who pursued SMA carrier testing remained favorable regarding this testing following disclosure of the results, ii) despite a lack of familiarity with SMA, there is interest in carrier screening for this condition, and iii) the information necessary for individuals to make informed decisions regarding carrier testing for SMA can be presented effectively and efficiently through counseling session(s) and printed educational material, such as those provided by patient advocacy groups such as the Claire Altman Heine Foundation, Inc. and Prevention of Spinal Muscular Atrophy (CAHF, http://www.clairealtmanheinefoundation.org/, last accessed August 15, 2010).11 Because this is the first reported study that included patient knowledge, attitudes, and assessment of existing education material, future pilot programs should be designed to gather additional data on carrier rates, refine risk estimates, optimize result reports, and develop educational materials for physicians and patients to facilitate pre- and posttest counseling. Development of educational materials and testing such material is a currently unmet prerequisite. An understanding of carrier status should be assessed immediately after screening and at a later point, to evaluate the accuracy of recollection of the meaning and significance of the results received. This will be a valuable tool in the assessment of feasibility, utility, and value of population carrier screening under various models.
3. Determine SMA Carrier Frequency in Different Ethnic Groups Ethnicity-specific information on SMA carrier frequencies is limited. Although SMA occurs in all populations, the carrier frequency in different ethnic groups appears to differ significantly. A recent study on SMA carrier frequencies12 indicates significant differences among the major ethnic groups of the United States, ranging from about 1 in 35 in whites to about 1 in 66 in African Americans, which could possibly be due to a chance variation. Replicative, large-scale, population-based studies are required to minimize sampling error and establish carrier frequencies among various ethnic populations. 4. Continue Research on SMA Genotype–Phenotype Correlations Currently, accurate prediction of the phenotype of a fetus with a homozygous deletion of SMN1 is not possible because an understanding of the molecular basis of the different types of SMA is incomplete and our ability to predict the severity of the disease, based on genotype, is limited. It has become clear that the phenotype is not only modulated by SMN2 copy number, but also by sequence differences between SMN2 genes.13 As with other disorders for which carrier screening has been implemented, continued research will be needed to better define genotype–phenotype correlations as well as gene– environment interactions that possibly influence the phenotype. This research should continue past the implementation of carrier screening and should inform these programs as more knowledge of the relationship between genotype and phenotype becomes available. Such an approach has proven to be successful for cystic fibrosis. 5. Improve SMA Risk Assessment In contrast to carrier screening for other conditions such as those associated with Ashkenazi Jewish ancestry or cystic fibrosis, the interpretation of SMA carrier testing is much more complex. Risk assessment of SMA (regardless of severity) is complicated by the presence of SMN copy number variations, small intragenic mutations, a relatively high de novo mutation rate, and the risk of falsenegative carrier screening.14 In addition, there is a paucity of data on the distribution of various disease and normal alleles in different ethnic groups. A particular challenge is that test results on additional family members can drastically change risk estimates for family members already tested. Genetic counselors, geneticists, and/or molecular diagnosticians who estimate carrier risks based on initial test results will need to be informed of all additional test results so that risk assessments can be adjusted accordingly. For families without a history of SMA, specific algorithms must be developed to enable consistent and correct risk estimates. Currently, expert evaluation that results in accurate carrier risk assessment is not widely available. This knowledge base and expertise must be integrated as part of the implementation of population carrier screening for SMA.
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6. Address SMA Carrier Test Licensing and Accessibility Laboratory testing is of primary importance for population-based SMA carrier screening. Testing for cystic fibrosis and Ashkenazi Jewish disease carrier status is widely available and performed in numerous laboratories. Carrier testing for SMA, on the other hand, is (nationally) only available from very few laboratories due to licensing issues. A test used for population-based screening, particularly screening advocated by professional organizations, should support widespread accessibility to patients, robust capacity, effective proficiency testing, continued innovation, and competitive pricing. Whether SMA carrier testing, as currently available, would meet such goals for a generalized population-based carrier screening is questionable. Although AMP/American Civil Liberty Union’s actions against gene patenting may resolve this issue in the future, concerns about accessibility and affordability of the test need to be seriously considered at the present time. Meanwhile, the absence of nonexclusive licenses for any lab that wishes to pay the fees remains an ethical dilemma.
Acknowledgments The Association for Molecular Pathology (AMP) is an international medical professional association that represents more than 1800 physicians, doctoral scientists, and medical technologists who perform laboratory testing based on knowledge derived from molecular biology, genetics, and genomics. Since the beginning of our organization, we have dedicated ourselves to the development and implementation of molecular diagnostic testing, which includes genetic testing in all its definitions, in a manner consistent with the highest standards established by the Clinical Laboratory Improvement Act (CLIA), the College of American Pathologists (CAP), the American College of Medical Genetics (ACMG), and the United States Food and Drug Administration (FDA). Our
members lead and work at the majority of clinical molecular diagnostic laboratories in the United States as well as in laboratories in many other countries.
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