- Email: [email protected]
Conveying a probabilistic genetic test result to families with an inherited heart disease
CONTEMPORARY REVIEW
Conveying a probabilistic genetic test result to families with an inherited heart disease Jodie Ingles, BBiomedSc, GradDipGenCouns, PhD,*† Christopher Semsarian, MBBS, PhD, FHRS*†‡ From the *Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia, †Sydney Medical School, University of Sydney, Sydney, Australia, and ‡Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia. The evolution of genetic testing in the past few years has been astounding. In a matter of only a few years, we now have comprehensive gene tests comprising vast panels of “cardiac” genes, whole exome sequencing (the entire coding region) and even whole genome sequencing (the entire genome). Making the call as to whether a DNA variant is causative or benign is difficult and the focus of intense research efforts. In most cases, the final answer will not be a simple yes/no outcome but rather a graded continuum of pathogenicity. This allows classification of variants in a more probabilistic way. How we convey this to a patient is the challenge, and certainly shines a spotlight on the important skills of the cardiac genetic counselor. This is an exciting step forward, but the overwhelming complexity of the information generated from these tests means our current practices of conveying genetic information to the family must be carefully considered. Despite the challenges, a genetic diagnosis in a family has great benefit
Introduction Recent advances in gene sequencing technologies have been phenomenal. Only a decade ago, the option of genetic testing for families with inherited heart diseases was minimal, typically requiring the sample to be sent to a research laboratory with a result expected to take at least 6 months. The commercialization of genetic tests for hypertrophic cardiomyopathy (HCM), long QT syndrome (LQTS), arrhythmogenic right ventricular cardiomyopathy (ARVC), catecholaminergic polymorphic ventricular tachycardia, and Brugada syndrome (BrS) evolved rapidly, and the increasing availability and uptake allowed a better understanding of the genetic basis of these diseases. Commercial testing laboratories offered limited panels of known causative genes for each disease, with a quoted mutation identification rate
Dr Ingles is the recipient of a National Health and Medical Research Council (NHMRC) and National Heart Foundation of Australia Early Career Fellowship (#1036756). Dr Semsarian is the recipient of an NHMRC Practitioner Fellowship (#1059156). Address reprint requests and correspondence: Dr Chris Semsarian, Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Locked Bag 6, Newtown, NSW 2042, Australia. E-mail address: [email protected].
1547-5271/$-see front matter B 2014 Heart Rhythm Society. All rights reserved.
both in reassuring unaffected family members and removing the need for lifetime clinical surveillance. The multidisciplinary specialized clinic model, incorporating genetic counselors, cardiologists and geneticists, provides the ideal framework for ensuring the best possible care for genetic heart disease families. KEYWORDS Genetic counseling; Genetic heart Multidisciplinary team; Next generation sequencing
disease;
ABBREVIATIONS ARVC ¼ arrhythmogenic right ventricular cardiomyopathy; BrS ¼ Brugada syndrome; HCM ¼ hypertrophic cardiomyopathy; LQTS ¼ long QT syndrome; SCD ¼ sudden cardiac death; VUS ¼ variant of uncertain significance; WES ¼ whole exome sequencing; WGS ¼ whole genome sequencing (Heart Rhythm 2014;11:1073–1078) I 2014 Heart Rhythm Society. All rights reserved.
between 20% and 75%, depending on the test and the specific disease in question. In this setting, testing was limited by the expense and time required to sequence 1 gene, and in many cases there were only 2 outcomes—either a causative (pathogenic) mutation could be found or it remained unidentified. In 2014 this is no longer the case. Next generation sequencing technologies have paved the way for testing of a vast number of genes, with a typical “cardiac gene chip” (or “panel”) now comprising 20–100 genes.1 No longer does a genetic test for HCM include only those genes previously shown to definitively cause disease but now includes a number of additional genes, many of which have only minimal evidence of disease association or causation (ie, accounting for o5% of disease). Whole exome sequencing (WES; sequencing of the entire coding region of the genome) and whole genome sequencing (WGS; sequencing of the entire genome) are powerful tools for research and gene discovery, but in the commercial setting expand testing beyond the scope of just evaluating cardiac-related genes, to sequencing of the remaining 22,000 genes encoded in our DNA. Coupled with rapidly decreasing costs and wider access and uptake, the complexity of the results generated http://dx.doi.org/10.1016/j.hrthm.2014.03.017
1074 Table 1
Heart Rhythm, Vol 11, No 6, June 2014 Probabilistic outcomes of cardiac genetic testing
Possible outcome
Consequences for the proband
No variants of potential clinical importance identified (benign) Variant of uncertain significance identified
An indeterminate gene result does not exclude a Predictive genetic testing cannot be offered to the cardiac genetic disease, but reassessment of the family. At-risk relatives are advised to be clinically phenotype should be considered assessed according to current guidelines Efforts to delineate pathogenicity of the variant are While pathogenicity of a variant is under question, it required, including cosegregation studies involving cannot be used to inform clinical management of phenotyped family members family members. Predictive genetic testing cannot be offered. At-risk relatives are advised to be clinically assessed according to guidelines Confirm clinical diagnosis and limited therapeutic and Predictive genetic testing of asymptomatic family members is available after genetic counseling prognostic application except in familial long QT syndrome3 Complex inheritance risk to first-degree relatives must be Confirm clinical diagnosis and potentially explain a discussed.5 Predictive genetic testing of asymptomatic more severe clinical phenotype.4–6 family members is available after genetic counseling Action regarding incidental or secondary findings must Genetic counseling to determine clinical and genetic be discussed with the proband pretest. effects to family members is available
Pathogenic mutation identified (pathogenic or likely pathogenic) Multiple pathogenic mutations identified Incidental or secondary pathogenic mutation identified
when a LQTS or HCM gene test is now ordered goes beyond the basic expertise and scope of current practices. The outcome of these genetic advances is that a proband genetic test should not be considered a binary (yes/no) outcome, but rather a complex and carefully considered result placed somewhere along a continuum from benign to variant of uncertain significance (VUS), probably/likely pathogenic, and pathogenic (Table 1). The genetic test result is therefore a probabilistic one, in which the weight of evidence for pathogenicity determines the likelihood (or probability) of the specific variant being disease causing. Adding a further layer of complexity, it is now evident that ongoing periodic reassessment is required to ensure new genetic information has not altered previous variant calls.2 Despite this, the clinical applicability of genetic testing within a family at risk of a cardiac genetic condition has significant power, with the ability to exclude asymptomatic family members from years of unnecessary clinical screening and to target those who carry a causative gene mutation to regular clinical surveillance. Finding a way to negotiate this new era of genomics and provide the best possible care to families remains the ultimate goal. This brief review highlights the challenges associated with conveying complex
Table 2
Consequences for the family
genetic information to families in the setting of inherited heart diseases.
The probabilistic genetic test result and the VUS The greatest clinical utility of genetic testing is when a pathogenic disease-causing mutation is identified. This enables cascade or predictive genetic testing to be undertaken in asymptomatic relatives, so that family members with and without the mutation can be identified. In up to 5% of cases, multiple (2 or more) pathogenic mutations may be identified and generally correlate with more severe disease.5,7,8 In some diseases, such as LQTS, the identification of a pathogenic mutation in a particular gene may also guide therapy and prognosis.9 Where there is uncertainty about the significance of a reported variant, the so-called VUS, the subsequent decision to offer predictive genetic testing to asymptomatic family members is not always clear to the clinician. Where a variant remains under a cloud of uncertainty, it should not be used for predictive genetic testing. If cascade family screening is performed on the basis of an incorrectly classified variant, then there is the real possibility of
Common characteristics of variant pathogenicity guidelines
Variant characteristic Variation type Frequency Functional data Region Conservation Family studies
High suspicion of causation Loss of function, de novo variant Absence or low frequency in race-matched control populations such as the 1000 Genomes Project. Allele frequency may take disease prevalence into account.17 Variant previously reported to be causative (with strong evidence of causation, ie, family cosegregation) In vivo functional data relating to the same variant Mutation exists in the essential protein domain (eg, transmembrane and binding site) Protein alignment across many species shows highly conserved position Where available, cosegregation data to demonstrate coinheritance with disease. Large family analysis provides greatest evidence of disease association
In silico analysis using predictive software programs such as SIFT (J. Craig Venter Institute, La Jolla, CA) and Polyphen2 (Harvard Medical School, Boston, MA) may provide supportive evidence for pathogenicity, relating to functional effects, conservation, and biochemical properties.
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incorrectly releasing family members from clinical screening. Case reports of pathogenic mutations being downgraded to benign polymorphisms commonly found in normal populations have made this a reality across a number of conditions.10–12 Unfortunately, a definitive method of variant classification does not exist, but there are a number of factors that, taken together, can give some level of confidence, such as cosegregation with disease, conservation across species, functional data and absence (or low frequency) in normal populations, and major exome and genome databases (Table 2).13 The use of in silico prediction platforms have limitations but may provide useful additional evidence of causation,14,15 and where large families are unavailable, the absence of the variant in large normal populations is increasingly important.16 Better defining and determining the best criteria for pathogenicity is currently an important research focus and the subject of many reviews.16–18 There will likely remain subtle variability between centers, and ongoing reassessment will see these criteria evolve as we continue to better understand this complex area. The recent development of pathogenicity “calculators,” in which the probability of pathogenicity of a variant is scored on the basis of parameters mentioned above, may provide an effective method of variant calling (M. Ackerman, communication, November 2013). Of critical importance for the clinician is an understanding that genetic medicine is evolving at an incredible pace, and mass sequencing of control and disease populations is expanding our current knowledge about the extent of normal variation within our genome. Currently, there are more than 8000 publicly available human exomes and genomes as part of the NHLBI Exome Sequence and 1000 Genome projects, providing unprecedented volumes of genetic information. Thus, periodic reassessment of all variants is not only necessary but essential in ensuring family members are appropriately managed.2 The important issue of who takes the responsibility for periodically reassessing pathogenicity of variants is not clear. However, it should be considered as a necessary aspect of undertaking genetic testing and certainly the proband should be made aware that there is a small chance that they will be recontacted at some time in the future should new information arise, which directly affects their genetic result. Increasing the likelihood of identifying pathogenic mutations is possible and may be the best approach to limiting the detection of a VUS. Genetic testing should be performed in accordance with the established recommendations, and this includes ensuring the proband has a definitive clinical diagnosis of disease and targeted sequencing of disease-associated genes only.3,19 A detailed family history is essential, as establishing familial inheritance can significantly increase mutation detection rates.19–21 A valuable contribution made by cardiac genetic counselors is to also coordinate and facilitate comprehensive clinical screening of the first-degree relatives.22 A well-characterized family has other advantages. If a VUS is identified then cosegregation analyses can be initiated to shed light on whether the variant identified is truly
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causative. Seeking participation of the wider family to assist with the clarification of a gene result offers a number of challenges and again highlights the value of incorporating cardiac genetic counselors in the entire genetic testing process.
Conveying a probabilistic genetic test result to the patient and their family The role of genetic counseling both pre- and postgenetic testing is increasingly critical in obtaining informed consent, ensuring the patient understands the test outcome and providing education and support.23,24 In the setting of cardiac genetics, many of the families are dealing with significant life events, including living with an implantable cardioverter-defibrillator and a family history of sudden cardiac death (SCD) or other serious cardiac events. The genetic counseling issues faced by these families are significant and unique, and there is a growing understanding of the effect this has on psychosocial well-being and healthrelated quality of life.25–27 These challenges have shaped the role of cardiac genetic counseling as a unique subspecialty, where pretest genetic counseling may be carried out at a time when a family is grieving28 or involve patients struggling to adapt to their implantable cardioverter-defibrillator.29,30 Despite the significant issues and potential emotional consequences in this group, studies have specifically evaluated the effect of genetic testing for cardiac genetic diseases and there is a general consensus that most patients cope well with this information.31–33 An important point to highlight, however, is that these studies were carried out before the next generation sequencing era, and the issues relating to delivery of a complex probabilistic genetic test result were not as apparent. The effect of the increasing complexity and, at times, uncertainty of genetic testing results is not yet fully known, but it is reasonable to assume that with appropriate genetic counseling and sensible use of the genetic diagnosis within the family, patients overall will continue to cope well. The basic principles of pretest counseling essentially remain unchanged, since the ultimate goal is to ensure patients and families fully understand the processes and consequences of the genetic test (Table 3).24 However, the inherent uncertainty of the gene result must be conveyed to the patient. This is not to say that the patient should be overwhelmed with an enormous amount of technical and genetic detail or be left with a bleak view of genetic testing. However, as it was a novel variant the testing laboratory reported it as “probably disease associated” and cautioned that it should not be used for predictive genetic testing unless co-inheritance can be established. Explaining that the identification of a VUS may require the initiation of further family investigation to clarify pathogenicity should be part of this discussion, and indeed a detailed family history at this point will give information about whether this is even possible. Furthermore, it should be highlighted clearly that there is a small chance that new information will become available in the future that may change the result. Trained genetic counselors are skilled in delivering complex
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Heart Rhythm, Vol 11, No 6, June 2014 Key points for pretest genetic counseling
Key point
Issues for discussion
Detailed family history
Collection or confirmation of the family pedigree is critical. This should identify information such as age, clinical status, and residential location of at-risk family members. An established family history of disease is likely to increase genetic test pickup rates18,19 Clear explanation of genetic inheritance of the disease Blood sample collection, type of genetic test (targeted gene panel, large cardiac panel, or whole exome or genome sequencing), turnaround time and cost, mode of delivery of result (phone, letter, or in person), and who will deliver result (cardiologist or genetic counselor) Detailed discussion of potential outcomes as shown in Table 1
Genetic education Process and logistics of testing and the result Explanation of all possible outcomes Clinical implications Genetic implications Risk of reclassification Incidental or secondary findings Explore feelings and understanding Insurance
Discussion of potential clinical implications of a gene result for the proband and family members Discussion of potential genetic implications of a gene result for the rest of the family. Giving a tailored description of the utility of predictive genetic testing for their family is helpful Families should be aware that there is a small chance that new information may alter the pathogenicity status of the variant identified Depending on the type of genetic test ordered, there is potential for pathogenic mutations to be identified in other genes. There must be a clear understanding and process for dealing with these before testing, and this must be carefully articulated to the proband Ask how they might feel about receiving any of these results. Determine how family communication and dynamics will allow this information to be passed on. Gauge level of understanding of the information presented Implications for obtaining insurance will vary by country
information in a sensitive manner, and these skills should be used in this setting. Genetic counselors with specific expertise in cardiac genetics can be located within the United States via the National Society of Genetic Counselors’s “find a genetic counselor” tool (www.nsgc.org).
Incidental findings
Incidental or secondary genetic findings are now real possible outcomes that can result from WES and WGS tests and present an ethically challenging area.34–36 In the most extreme circumstances, this will include the testing laboratory reporting important variants in noncardiac genes (eg, familial cancer genes) and therefore giving information completely unrelated to the purpose of the gene test. This is not dissimilar to incidental clinical findings, such as the discovery of a breast lump during a cardiac magnetic resonance imaging study. But this issue of incidental genetic findings is not just limited to whole genome approaches. If a patient has a clear HCM phenotype and upon genetic testing via a cardiac gene chip a LQTS mutation is identified, then this too raises a number of issues, namely, in determining the clinical relevance of the LQTS variant in a patient with an HCM phenotype. While genotype/phenotype crossover may occur among the genetic heart diseases, for example, mutations in the sodium channel gene SCN5A can cause LQTS, BrS, and primary conduction disease, a first-line genetic test that includes screening of every cardiac disease gene known may not be the best approach, but is now a reality. Furthermore, recent whole genome studies in patients with BrS suggest that a cumulative effect of both rare and common genetic variants may collectively cause disease in an individual patient.37 Testing for disease modifiers currently remains within a research setting, though some show great promise for translation into research practice.38–40
Given these current and emerging complexities, all probands undergoing cardiac gene chip-based genetic testing should be aware of the potential for variants in other cardiac diseases to be reported, and this needs to be part of the pretest counseling discussion. Similarly, clinicians ordering these tests should be clear about how such a result might alter their patient’s management and decide which method of genetic testing is most appropriate and clinically relevant for their patient. In contrast, a growing referral group to cardiac genetic services will be those with no cardiac phenotype who have a pathogenic or likely pathogenic mutation identified after clinical exome sequencing for a noncardiac indication. This poses a significant challenge with potential to overburden already stretched cardiac genetic services. The best approach for dealing with such cases remains unclear, but there is an understanding that the presence of a gene mutation does not always translate to a clinical phenotype and patient management should be centered on clinical phenotype.41 Assessment of such families will require expertise in cardiac genetics and likely input from the entire multidisciplinary team (including the genetic counselor, clinical geneticist, cardiologist, genetic testing centers, and research laboratory). A less commonly discussed issue is that of incidental findings arising from genetic studies in the research setting.42,43 With mutation detection rates very much incomplete, the role of new gene discovery research is essential in further defining the genetic causes of heart disease. Next generation sequencing technology has afforded researchers a powerful tool, allowing a move away from candidate gene approaches to detailed WES and WGS bioinformatic analyses. In filtering and sorting deleterious variants arising from this analysis, it is plausible and perhaps likely that pathogenic mutations in noncardiac genes will unavoidably be identified. Whether individual research groups should report
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back incidental findings needs to be established, and this will be affected by a host of factors such as the type of research laboratory and existing human ethics protocols. Regardless, informed consent for participation in the study must include full disclosure of the purpose and potential direct outcomes of the research to the participant, including the possibility of incidental findings, and how these will be dealt with. Some individuals may choose to receive only cardiac-related genetic data. Importantly, many cardiac genetic counselors work within the research setting, and it is reasonable that some level of counseling be incorporated into the informed consent process for human genetic research studies where there is potential for significant implications for the research participants.
described in LQTS, and there is adequate biological and functional data to support causation, including in silico support, while the DSP variant was reported to occur in the general population at a frequency of up to 1%. The cardiac genetic counselor clearly explained the status of each variant, and it was decided that the family would be tested for the KCNE1 mutation and have ongoing evaluation for both ARVC and LQTS. The proband will continue to be managed according to his clinical phenotype of ARVC as well as be informed of simple measures of avoiding QT-prolonging drugs. This scenario highlights the challenges of finding multiple DNA variants in cardiac genes and the key role of comprehensive phenotyping of patients and their at-risk relatives.
Illustrative cases
Case 3
While these are complex scenarios best dealt with on a caseby-case basis by centers with expertise in cardiac genetics,44 the following illustrative cases highlight some key principles in the evaluation of genetic findings in the clinical context.
A family presented to a specialized cardiac genetic service after the identification of a VUS in AKAP9 (LQTS11), an incidental finding from clinical exome testing performed to clarify the genetic cause of a neurological hereditary chorea in the family. The family underwent comprehensive cardiac assessment, and no members were found to have any evidence of LQTS. After discussion with the family, they were reassured that the AKAP9 variant is unlikely to be of clinical importance and no further investigation was recommended. This case highlights the emerging issue of “incidental findings,” particularly in the setting of clinical exome or genome testing. Again, detailed clinical phenotyping is critical in the interpretation of incidental findings.
Case 1 A 45-year-old man presented with a clinical diagnosis of mild HCM with a left ventricular wall thickness of 15 mm and a family history of SCD of his father aged 30 years. Commercial genetic testing of a “panel” of 10 HCM genes was performed and a novel variant Ile1160Fs MYBPC3 identified. This variant causes a novel insertion resulting in a frameshift likely leading to a loss of function of the protein, which provides additional support for disease causation. However, it was never reported before the testing laboratory reported it as “probably disease associated” and cautioned that it should not be used for predictive genetic testing unless coinheritance can be established. Fortunately, the proband’s first cousin was known to be clinically affected and willing to provide a DNA sample after discussion with the cardiac genetic counselor. The variant was subsequently confirmed in the cousin, and although there is a small chance that cosegregation occurred by chance, taking into consideration the strong functional evidence, the pathogenicity status was upgraded to allow testing of the family. Cosegregation of the genetic variant with disease in the context of a family is a key factor in determining pathogenicity.
Case 2 A 30-year-old man presented with a clinical diagnosis of ARVC based on 2010 task force criteria45 after a resuscitated cardiac arrest. Full cardiac evaluation did not reveal any additional findings, including a normal corrected QT interval (415 ms). A detailed family history revealed no history of cardiac disease or SCD, and this was confirmed after clinical screening of his sibling and parents, which included cardiac magnetic resonance imaging. The proband underwent a “chip-based” cardiac genetic test (approximately 60 cardiac genes), and a “likely pathogenic” mutation in KCNE1 Asp76Asn (LQT5) and a VUS in DSP Arg1537Cys (ARVC) were identified. The KCNE1 mutation has previously been
Future challenges The role of the cardiac genetic counselor as the interface between this complex genetic information and the families is increasingly important, particularly in the setting of pretest genetic counseling, where the goal is to ensure patients and their families are fully equipped and informed to make the best decision for their circumstances. Of equal importance is the role of the cardiologist in ensuring comprehensive phenotyping of the proband and clinical evaluation of firstdegree relatives before genetic testing. The multidisciplinary approach incorporating genetic counseling, cardiology, and expertise from many other fields is therefore the ideal model to deliver care. This is an area that will only continue to expand, both in accessibility to the wider disease population and in the number of genetic variants requiring interpretation. Furthermore, as continued research efforts shed light on the effect of gene modifiers, the potential for clinicians to better predict outcomes through genetics may be within reach. While targeted gene approaches may be a simpler solution, the reality is that large gene chip-based tests, clinical exome sequencing, and WGS are here. As we struggle to understand what this wealth of information means to cardiac genetic disease states in a clinical setting, from a research perspective the possibilities are endless. Despite the uncertainty and issues, it cannot be underestimated how incredibly powerful
1078 a genetic diagnosis can be for these families if carried out appropriately. Seamless collaboration and communication within the multidisciplinary team, including the cardiologist, genetic counselor, clinical geneticist, commercial testing center, and research laboratories will be the key to ensuring probabilistic genetic results are correctly conveyed, facilitating the effective and high-quality care of families with cardiac genetic diseases.
References 1. Sturm AC, Hershberger RE. Genetic testing in cardiovascular medicine: current landscape and future horizons. Curr Opin Cardiol 2013;28:317–325. 2. Das KJ, Ingles J, Bagnall RD, Semsarian C. Determining pathogenicity of genetic variants in hypertrophic cardiomyopathy: importance of periodic reassessment. Genet Med 2013;16(4):286–293. 3. Ackerman MJ, Priori SG, Willems S, et al. HRS/EHRA expert consensus statement on the state of genetic testing for the channelopathies and cardiomyopathies this document was developed as a partnership between the Heart Rhythm Society (HRS) and the European Heart Rhythm Association (EHRA). Heart Rhythm 2011;8:1308–1339. 4. Maron BJ, Maron MS, Semsarian C. Double or compound sarcomere mutations in hypertrophic cardiomyopathy: a potential link to sudden death in the absence of conventional risk factors. Heart Rhythm 2012;9:57–63. 5. Ingles J, Doolan A, Chiu C, Seidman J, Seidman C, Semsarian C. Compound and double mutations in patients with hypertrophic cardiomyopathy: implications for genetic testing and counselling. J Med Genet 2005;42:e59. 6. Bauce B, Nava A, Beffagna G, et al. Multiple mutations in desmosomal proteins encoding genes in arrhythmogenic right ventricular cardiomyopathy/dysplasia. Heart Rhythm 2010;7:22–29. 7. Kelly M, Semsarian C. Multiple mutations in genetic cardiovascular disease: a marker of disease severity? Circ Cardiovasc Genet 2009;2:182–190. 8. Girolami F, Ho CY, Semsarian C, Baldi M, Will ML, Baldini K, Torricelli F, Yeates L, Cecchi F, Ackerman MJ, Olivotto I. Clinical features and outcome of hypertrophic cardiomyopathy associated with triple sarcomere protein gene mutations. J Am Coll Cardiol 2010;55:1444–1453. 9. Schwartz PJ, Priori SG, Spazzolini C, et al. Genotype-phenotype correlation in the long-QT syndrome: gene-specific triggers for life-threatening arrhythmias. Circulation 2001;103:89–95. 10. Kapplinger J, Tester DJ, Ackerman MJ. The compounding dilemma of genetic noise: identification of the genetic noise rate in genes associated with cardiac channelopathies. Heart Rhythm 2013;10:1752–1753. 11. Jabbari J, Jabbari R, Nielsen MW, Holst AG, Nielsen JB, Haunso S, Tfelt-Hansen J, Svendsen JH, Olesen MS. New exome data question the pathogenicity of genetic variants previously associated with catecholaminergic polymorphic ventricular tachycardia. Circ Cardiovasc Genet 2013;6:481–489. 12. Andreasen C, Nielsen JB, Refsgaard L, Holst AG, Christensen AH, Andreasen L, Sajadieh A, Haunso S, Svendsen JH, Olesen MS. New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants. Eur J Hum Genet 2013;21:918–928. 13. Maron BJ, Maron MS, Semsarian C. Genetics of hypertrophic cardiomyopathy after 20 years: clinical perspectives. J Am Coll Cardiol 2012;60:705–715. 14. Pan S, Caleshu CA, Dunn KE, Foti MJ, Moran MK, Soyinka O, Ashley EA. Cardiac structural and sarcomere genes associated with cardiomyopathy exhibit marked intolerance of genetic variation. Circ Cardiovasc Genet 2012;5:602–610. 15. Tennessen JA, Bigham AW, O’Connor TD, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012;337:64–69. 16. Marian AJ. Causality in genetics: the gradient of genetic effects and back to koch postulates of causality. Circ Res 2014;114:e18–e21. 17. Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG. Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet 2013;6:337–346. 18. Ohanian M, Otway R, Fatkin D. Heuristic methods for finding pathogenic variants in gene coding sequences. J Am Heart Assoc 2012;1:e002642. 19. Hofman N, Tan HL, Alders M, Kolder I, de Haij S, Mannens MM, Lombardi MP, Dit Deprez RH, van Langen I, Wilde AA. Yield of molecular and clinical testing for arrhythmia syndromes: report of 15 years’ experience. Circulation 2013;128: 1513–1521. 20. Ingles J, Sarina T, Yeates L, Hunt L, Macciocca I, McCormack L, Winship I, McGaughran J, Atherton J, Semsarian C. Clinical predictors of genetic
Heart Rhythm, Vol 11, No 6, June 2014
21.
22. 23. 24.
25.
26.
27.
28.
29.
30.
31.
32.
33. 34. 35.
36. 37.
38.
39.
40.
41.
42.
43.
44. 45.
testing outcomes in hypertrophic cardiomyopathy. Genet Med 2013;15(12): 972–977. Gruner C, Ivanov J, Care M, Williams L, Moravsky G, Yang H, Laczay B, Siminovitch K, Woo A, Rakowski H. Toronto hypertrophic cardiomyopathy genotype score for prediction of a positive genotype in hypertrophic cardiomyopathy. Circ Cardiovasc Genet 2013;6:19–26. Ingles J, Yeates L, Semsarian C. The emerging role of the cardiac genetic counselor. Heart Rhythm 2011;8:1958–1962. Biesecker B. Goals of genetic counselling. Clin Genet 2001;60:323–330. Resta R, Biesecker BB, Bennett RL, Blum S, Hahn SE, Strecker MN, Williams JL. A new definition of genetic counseling: National Society of Genetic Counselors’ Task Force report. J. Genet Counsel 2006;15:77–83. Christiaans I, van Langen IM, Birnie E, Bonsel GJ, Wilde AA, Smets EM. Quality of life and psychological distress in hypertrophic cardiomyopathy mutation carriers: a cross-sectional cohort study. Am J Med Genet A 2009;149A:602–612. Ormondroyd E, Oates S, Parker M, Blair E, Watkins H. Pre-symptomatic genetic testing for inherited cardiac conditions: a qualitative exploration of psychosocial and ethical implications. Eur J Hum Genet 2013;22(1):88–93. Ingles J, Yeates L, Hunt L, McGaughran J, Scuffham PA, Atherton J, Semsarian C. Health status of cardiac genetic disease patients and their at-risk relatives. Int J Cardiol 2013;165:448–453. Yeates L, Hunt L, Saleh M, Semsarian C, Ingles J. Poor psychological wellbeing particularly in mothers following sudden cardiac death in the young. Eur J Cardiovasc Nurs 2013;12:484–491. Ingles J, Sarina T, Kasparian N, Semsarian C. Psychological wellbeing and posttraumatic stress associated with implantable cardioverter defibrillator therapy in young adults with genetic heart disease. Int J Cardiol 2013;168:3779–3784. James CA, Tichnell C, Murray B, Daly A, Sears SF, Calkins H. General and disease-specific psychosocial adjustment in patients with arrhythmogenic right ventricular dysplasia/cardiomyopathy with implantable cardioverter defibrillators: a large cohort study. Circ Cardiovasc Genet 2012;5:18–24. Ingles J, Yeates L, O’Brien L, McGaughran J, Scuffham PA, Atherton J, Semsarian C. Genetic testing for inherited heart diseases: longitudinal impact on health-related quality of life. Genet Med 2012; Epub May 3. Christiaans I, van Langen IM, Birnie E, Bonsel GJ, Wilde AA, Smets EM. Genetic counseling and cardiac care in predictively tested hypertrophic cardiomyopathy mutation carriers: the patients’ perspective. Am J Med Genet A 2009;149A:1444–1451. Aatre RD, Day SM. Psychological issues in genetic testing for inherited cardiovascular diseases. Circ Cardiovasc Genet 2011;4:81–90. Green RC, Lupski JR, Biesecker LG. Reporting genomic sequencing results to ordering clinicians: incidental, but not exceptional. JAMA 2013;310:365–366. Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013; 15:565–574. Grove ME, Wolpert MN, Cho MK, Lee SS, Ormond KE. Views of genetics health professionals on the return of genomic results. J Genet Counsel 2013;Epub June 2. Bezzina CR, Barc J, Mizusawa Y, et al. Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death. Nat Genet 2013;45:1044–1049. Crotti L, Monti MC, Insolia R, Peljto A, Goosen A, Brink PA, Greenberg DA, Schwartz PJ, George AL Jr. NOS1AP is a genetic modifier of the long-QT syndrome. Circulation 2009;120:1657–1663. Crotti L, Hu D, Barajas-Martinez H, et al. Torsades de pointes following acute myocardial infarction: evidence for a deadly link with a common genetic variant. Heart Rhythm 2012;9:1104–1112. Hu D, Barajas-Martinez H, Medeiros-Domingo A, et al. A novel rare variant in SCN1Bb linked to Brugada syndrome and SIDS by combined modulation of Na (v)1.5 and K(v)4.3 channel currents. Heart Rhythm 2012;9:760–769. Ploski R, Pollak A, Muller S, Franaszczyk M, Michalak E, Kosinska J, Stawinski P, Spiewak M, Seggewiss H, Bilinska ZT. Does p.Q247X in TRIM63 cause human hypertrophic cardiomyopathy? Circ Res 2014;114:e2–e5. Appelbaum PS, Waldman CR, Fyer A, Klitzman R, Parens E, Martinez J, Price WN II, Chung WK. Informed consent for return of incidental findings in genomic research. Genet Med 2013; Epub Oct 24. Klitzman R, Buquez B, Appelbaum PS, Fyer A, Chung WK. Processes and factors involved in decisions regarding return of incidental genomic findings in research. Genet Med 2013; 16(4):311–317. Caleshu C, Day S, Rehm HL, Baxter S. Use and interpretation of genetic tests in cardiovascular genetics. Heart 2010;96:1669–1675. Marcus FI, McKenna WJ, Sherrill D, et al. Diagnosis of arrhythmogenic right ventricular cardiomyopathy/dysplasia: proposed modification of the task force criteria. Circulation 2010;121:1533–1541.
Conveying a probabilistic genetic test result to families with an inherited heart disease Jodie Ingles, BBiomedSc, GradDipGenCouns, PhD,*† Christopher Semsarian, MBBS, PhD, FHRS*†‡ From the *Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia, †Sydney Medical School, University of Sydney, Sydney, Australia, and ‡Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia. The evolution of genetic testing in the past few years has been astounding. In a matter of only a few years, we now have comprehensive gene tests comprising vast panels of “cardiac” genes, whole exome sequencing (the entire coding region) and even whole genome sequencing (the entire genome). Making the call as to whether a DNA variant is causative or benign is difficult and the focus of intense research efforts. In most cases, the final answer will not be a simple yes/no outcome but rather a graded continuum of pathogenicity. This allows classification of variants in a more probabilistic way. How we convey this to a patient is the challenge, and certainly shines a spotlight on the important skills of the cardiac genetic counselor. This is an exciting step forward, but the overwhelming complexity of the information generated from these tests means our current practices of conveying genetic information to the family must be carefully considered. Despite the challenges, a genetic diagnosis in a family has great benefit
Introduction Recent advances in gene sequencing technologies have been phenomenal. Only a decade ago, the option of genetic testing for families with inherited heart diseases was minimal, typically requiring the sample to be sent to a research laboratory with a result expected to take at least 6 months. The commercialization of genetic tests for hypertrophic cardiomyopathy (HCM), long QT syndrome (LQTS), arrhythmogenic right ventricular cardiomyopathy (ARVC), catecholaminergic polymorphic ventricular tachycardia, and Brugada syndrome (BrS) evolved rapidly, and the increasing availability and uptake allowed a better understanding of the genetic basis of these diseases. Commercial testing laboratories offered limited panels of known causative genes for each disease, with a quoted mutation identification rate
Dr Ingles is the recipient of a National Health and Medical Research Council (NHMRC) and National Heart Foundation of Australia Early Career Fellowship (#1036756). Dr Semsarian is the recipient of an NHMRC Practitioner Fellowship (#1059156). Address reprint requests and correspondence: Dr Chris Semsarian, Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Locked Bag 6, Newtown, NSW 2042, Australia. E-mail address: [email protected].
1547-5271/$-see front matter B 2014 Heart Rhythm Society. All rights reserved.
both in reassuring unaffected family members and removing the need for lifetime clinical surveillance. The multidisciplinary specialized clinic model, incorporating genetic counselors, cardiologists and geneticists, provides the ideal framework for ensuring the best possible care for genetic heart disease families. KEYWORDS Genetic counseling; Genetic heart Multidisciplinary team; Next generation sequencing
disease;
ABBREVIATIONS ARVC ¼ arrhythmogenic right ventricular cardiomyopathy; BrS ¼ Brugada syndrome; HCM ¼ hypertrophic cardiomyopathy; LQTS ¼ long QT syndrome; SCD ¼ sudden cardiac death; VUS ¼ variant of uncertain significance; WES ¼ whole exome sequencing; WGS ¼ whole genome sequencing (Heart Rhythm 2014;11:1073–1078) I 2014 Heart Rhythm Society. All rights reserved.
between 20% and 75%, depending on the test and the specific disease in question. In this setting, testing was limited by the expense and time required to sequence 1 gene, and in many cases there were only 2 outcomes—either a causative (pathogenic) mutation could be found or it remained unidentified. In 2014 this is no longer the case. Next generation sequencing technologies have paved the way for testing of a vast number of genes, with a typical “cardiac gene chip” (or “panel”) now comprising 20–100 genes.1 No longer does a genetic test for HCM include only those genes previously shown to definitively cause disease but now includes a number of additional genes, many of which have only minimal evidence of disease association or causation (ie, accounting for o5% of disease). Whole exome sequencing (WES; sequencing of the entire coding region of the genome) and whole genome sequencing (WGS; sequencing of the entire genome) are powerful tools for research and gene discovery, but in the commercial setting expand testing beyond the scope of just evaluating cardiac-related genes, to sequencing of the remaining 22,000 genes encoded in our DNA. Coupled with rapidly decreasing costs and wider access and uptake, the complexity of the results generated http://dx.doi.org/10.1016/j.hrthm.2014.03.017
1074 Table 1
Heart Rhythm, Vol 11, No 6, June 2014 Probabilistic outcomes of cardiac genetic testing
Possible outcome
Consequences for the proband
No variants of potential clinical importance identified (benign) Variant of uncertain significance identified
An indeterminate gene result does not exclude a Predictive genetic testing cannot be offered to the cardiac genetic disease, but reassessment of the family. At-risk relatives are advised to be clinically phenotype should be considered assessed according to current guidelines Efforts to delineate pathogenicity of the variant are While pathogenicity of a variant is under question, it required, including cosegregation studies involving cannot be used to inform clinical management of phenotyped family members family members. Predictive genetic testing cannot be offered. At-risk relatives are advised to be clinically assessed according to guidelines Confirm clinical diagnosis and limited therapeutic and Predictive genetic testing of asymptomatic family members is available after genetic counseling prognostic application except in familial long QT syndrome3 Complex inheritance risk to first-degree relatives must be Confirm clinical diagnosis and potentially explain a discussed.5 Predictive genetic testing of asymptomatic more severe clinical phenotype.4–6 family members is available after genetic counseling Action regarding incidental or secondary findings must Genetic counseling to determine clinical and genetic be discussed with the proband pretest. effects to family members is available
Pathogenic mutation identified (pathogenic or likely pathogenic) Multiple pathogenic mutations identified Incidental or secondary pathogenic mutation identified
when a LQTS or HCM gene test is now ordered goes beyond the basic expertise and scope of current practices. The outcome of these genetic advances is that a proband genetic test should not be considered a binary (yes/no) outcome, but rather a complex and carefully considered result placed somewhere along a continuum from benign to variant of uncertain significance (VUS), probably/likely pathogenic, and pathogenic (Table 1). The genetic test result is therefore a probabilistic one, in which the weight of evidence for pathogenicity determines the likelihood (or probability) of the specific variant being disease causing. Adding a further layer of complexity, it is now evident that ongoing periodic reassessment is required to ensure new genetic information has not altered previous variant calls.2 Despite this, the clinical applicability of genetic testing within a family at risk of a cardiac genetic condition has significant power, with the ability to exclude asymptomatic family members from years of unnecessary clinical screening and to target those who carry a causative gene mutation to regular clinical surveillance. Finding a way to negotiate this new era of genomics and provide the best possible care to families remains the ultimate goal. This brief review highlights the challenges associated with conveying complex
Table 2
Consequences for the family
genetic information to families in the setting of inherited heart diseases.
The probabilistic genetic test result and the VUS The greatest clinical utility of genetic testing is when a pathogenic disease-causing mutation is identified. This enables cascade or predictive genetic testing to be undertaken in asymptomatic relatives, so that family members with and without the mutation can be identified. In up to 5% of cases, multiple (2 or more) pathogenic mutations may be identified and generally correlate with more severe disease.5,7,8 In some diseases, such as LQTS, the identification of a pathogenic mutation in a particular gene may also guide therapy and prognosis.9 Where there is uncertainty about the significance of a reported variant, the so-called VUS, the subsequent decision to offer predictive genetic testing to asymptomatic family members is not always clear to the clinician. Where a variant remains under a cloud of uncertainty, it should not be used for predictive genetic testing. If cascade family screening is performed on the basis of an incorrectly classified variant, then there is the real possibility of
Common characteristics of variant pathogenicity guidelines
Variant characteristic Variation type Frequency Functional data Region Conservation Family studies
High suspicion of causation Loss of function, de novo variant Absence or low frequency in race-matched control populations such as the 1000 Genomes Project. Allele frequency may take disease prevalence into account.17 Variant previously reported to be causative (with strong evidence of causation, ie, family cosegregation) In vivo functional data relating to the same variant Mutation exists in the essential protein domain (eg, transmembrane and binding site) Protein alignment across many species shows highly conserved position Where available, cosegregation data to demonstrate coinheritance with disease. Large family analysis provides greatest evidence of disease association
In silico analysis using predictive software programs such as SIFT (J. Craig Venter Institute, La Jolla, CA) and Polyphen2 (Harvard Medical School, Boston, MA) may provide supportive evidence for pathogenicity, relating to functional effects, conservation, and biochemical properties.
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incorrectly releasing family members from clinical screening. Case reports of pathogenic mutations being downgraded to benign polymorphisms commonly found in normal populations have made this a reality across a number of conditions.10–12 Unfortunately, a definitive method of variant classification does not exist, but there are a number of factors that, taken together, can give some level of confidence, such as cosegregation with disease, conservation across species, functional data and absence (or low frequency) in normal populations, and major exome and genome databases (Table 2).13 The use of in silico prediction platforms have limitations but may provide useful additional evidence of causation,14,15 and where large families are unavailable, the absence of the variant in large normal populations is increasingly important.16 Better defining and determining the best criteria for pathogenicity is currently an important research focus and the subject of many reviews.16–18 There will likely remain subtle variability between centers, and ongoing reassessment will see these criteria evolve as we continue to better understand this complex area. The recent development of pathogenicity “calculators,” in which the probability of pathogenicity of a variant is scored on the basis of parameters mentioned above, may provide an effective method of variant calling (M. Ackerman, communication, November 2013). Of critical importance for the clinician is an understanding that genetic medicine is evolving at an incredible pace, and mass sequencing of control and disease populations is expanding our current knowledge about the extent of normal variation within our genome. Currently, there are more than 8000 publicly available human exomes and genomes as part of the NHLBI Exome Sequence and 1000 Genome projects, providing unprecedented volumes of genetic information. Thus, periodic reassessment of all variants is not only necessary but essential in ensuring family members are appropriately managed.2 The important issue of who takes the responsibility for periodically reassessing pathogenicity of variants is not clear. However, it should be considered as a necessary aspect of undertaking genetic testing and certainly the proband should be made aware that there is a small chance that they will be recontacted at some time in the future should new information arise, which directly affects their genetic result. Increasing the likelihood of identifying pathogenic mutations is possible and may be the best approach to limiting the detection of a VUS. Genetic testing should be performed in accordance with the established recommendations, and this includes ensuring the proband has a definitive clinical diagnosis of disease and targeted sequencing of disease-associated genes only.3,19 A detailed family history is essential, as establishing familial inheritance can significantly increase mutation detection rates.19–21 A valuable contribution made by cardiac genetic counselors is to also coordinate and facilitate comprehensive clinical screening of the first-degree relatives.22 A well-characterized family has other advantages. If a VUS is identified then cosegregation analyses can be initiated to shed light on whether the variant identified is truly
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causative. Seeking participation of the wider family to assist with the clarification of a gene result offers a number of challenges and again highlights the value of incorporating cardiac genetic counselors in the entire genetic testing process.
Conveying a probabilistic genetic test result to the patient and their family The role of genetic counseling both pre- and postgenetic testing is increasingly critical in obtaining informed consent, ensuring the patient understands the test outcome and providing education and support.23,24 In the setting of cardiac genetics, many of the families are dealing with significant life events, including living with an implantable cardioverter-defibrillator and a family history of sudden cardiac death (SCD) or other serious cardiac events. The genetic counseling issues faced by these families are significant and unique, and there is a growing understanding of the effect this has on psychosocial well-being and healthrelated quality of life.25–27 These challenges have shaped the role of cardiac genetic counseling as a unique subspecialty, where pretest genetic counseling may be carried out at a time when a family is grieving28 or involve patients struggling to adapt to their implantable cardioverter-defibrillator.29,30 Despite the significant issues and potential emotional consequences in this group, studies have specifically evaluated the effect of genetic testing for cardiac genetic diseases and there is a general consensus that most patients cope well with this information.31–33 An important point to highlight, however, is that these studies were carried out before the next generation sequencing era, and the issues relating to delivery of a complex probabilistic genetic test result were not as apparent. The effect of the increasing complexity and, at times, uncertainty of genetic testing results is not yet fully known, but it is reasonable to assume that with appropriate genetic counseling and sensible use of the genetic diagnosis within the family, patients overall will continue to cope well. The basic principles of pretest counseling essentially remain unchanged, since the ultimate goal is to ensure patients and families fully understand the processes and consequences of the genetic test (Table 3).24 However, the inherent uncertainty of the gene result must be conveyed to the patient. This is not to say that the patient should be overwhelmed with an enormous amount of technical and genetic detail or be left with a bleak view of genetic testing. However, as it was a novel variant the testing laboratory reported it as “probably disease associated” and cautioned that it should not be used for predictive genetic testing unless co-inheritance can be established. Explaining that the identification of a VUS may require the initiation of further family investigation to clarify pathogenicity should be part of this discussion, and indeed a detailed family history at this point will give information about whether this is even possible. Furthermore, it should be highlighted clearly that there is a small chance that new information will become available in the future that may change the result. Trained genetic counselors are skilled in delivering complex
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Heart Rhythm, Vol 11, No 6, June 2014 Key points for pretest genetic counseling
Key point
Issues for discussion
Detailed family history
Collection or confirmation of the family pedigree is critical. This should identify information such as age, clinical status, and residential location of at-risk family members. An established family history of disease is likely to increase genetic test pickup rates18,19 Clear explanation of genetic inheritance of the disease Blood sample collection, type of genetic test (targeted gene panel, large cardiac panel, or whole exome or genome sequencing), turnaround time and cost, mode of delivery of result (phone, letter, or in person), and who will deliver result (cardiologist or genetic counselor) Detailed discussion of potential outcomes as shown in Table 1
Genetic education Process and logistics of testing and the result Explanation of all possible outcomes Clinical implications Genetic implications Risk of reclassification Incidental or secondary findings Explore feelings and understanding Insurance
Discussion of potential clinical implications of a gene result for the proband and family members Discussion of potential genetic implications of a gene result for the rest of the family. Giving a tailored description of the utility of predictive genetic testing for their family is helpful Families should be aware that there is a small chance that new information may alter the pathogenicity status of the variant identified Depending on the type of genetic test ordered, there is potential for pathogenic mutations to be identified in other genes. There must be a clear understanding and process for dealing with these before testing, and this must be carefully articulated to the proband Ask how they might feel about receiving any of these results. Determine how family communication and dynamics will allow this information to be passed on. Gauge level of understanding of the information presented Implications for obtaining insurance will vary by country
information in a sensitive manner, and these skills should be used in this setting. Genetic counselors with specific expertise in cardiac genetics can be located within the United States via the National Society of Genetic Counselors’s “find a genetic counselor” tool (www.nsgc.org).
Incidental findings
Incidental or secondary genetic findings are now real possible outcomes that can result from WES and WGS tests and present an ethically challenging area.34–36 In the most extreme circumstances, this will include the testing laboratory reporting important variants in noncardiac genes (eg, familial cancer genes) and therefore giving information completely unrelated to the purpose of the gene test. This is not dissimilar to incidental clinical findings, such as the discovery of a breast lump during a cardiac magnetic resonance imaging study. But this issue of incidental genetic findings is not just limited to whole genome approaches. If a patient has a clear HCM phenotype and upon genetic testing via a cardiac gene chip a LQTS mutation is identified, then this too raises a number of issues, namely, in determining the clinical relevance of the LQTS variant in a patient with an HCM phenotype. While genotype/phenotype crossover may occur among the genetic heart diseases, for example, mutations in the sodium channel gene SCN5A can cause LQTS, BrS, and primary conduction disease, a first-line genetic test that includes screening of every cardiac disease gene known may not be the best approach, but is now a reality. Furthermore, recent whole genome studies in patients with BrS suggest that a cumulative effect of both rare and common genetic variants may collectively cause disease in an individual patient.37 Testing for disease modifiers currently remains within a research setting, though some show great promise for translation into research practice.38–40
Given these current and emerging complexities, all probands undergoing cardiac gene chip-based genetic testing should be aware of the potential for variants in other cardiac diseases to be reported, and this needs to be part of the pretest counseling discussion. Similarly, clinicians ordering these tests should be clear about how such a result might alter their patient’s management and decide which method of genetic testing is most appropriate and clinically relevant for their patient. In contrast, a growing referral group to cardiac genetic services will be those with no cardiac phenotype who have a pathogenic or likely pathogenic mutation identified after clinical exome sequencing for a noncardiac indication. This poses a significant challenge with potential to overburden already stretched cardiac genetic services. The best approach for dealing with such cases remains unclear, but there is an understanding that the presence of a gene mutation does not always translate to a clinical phenotype and patient management should be centered on clinical phenotype.41 Assessment of such families will require expertise in cardiac genetics and likely input from the entire multidisciplinary team (including the genetic counselor, clinical geneticist, cardiologist, genetic testing centers, and research laboratory). A less commonly discussed issue is that of incidental findings arising from genetic studies in the research setting.42,43 With mutation detection rates very much incomplete, the role of new gene discovery research is essential in further defining the genetic causes of heart disease. Next generation sequencing technology has afforded researchers a powerful tool, allowing a move away from candidate gene approaches to detailed WES and WGS bioinformatic analyses. In filtering and sorting deleterious variants arising from this analysis, it is plausible and perhaps likely that pathogenic mutations in noncardiac genes will unavoidably be identified. Whether individual research groups should report
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back incidental findings needs to be established, and this will be affected by a host of factors such as the type of research laboratory and existing human ethics protocols. Regardless, informed consent for participation in the study must include full disclosure of the purpose and potential direct outcomes of the research to the participant, including the possibility of incidental findings, and how these will be dealt with. Some individuals may choose to receive only cardiac-related genetic data. Importantly, many cardiac genetic counselors work within the research setting, and it is reasonable that some level of counseling be incorporated into the informed consent process for human genetic research studies where there is potential for significant implications for the research participants.
described in LQTS, and there is adequate biological and functional data to support causation, including in silico support, while the DSP variant was reported to occur in the general population at a frequency of up to 1%. The cardiac genetic counselor clearly explained the status of each variant, and it was decided that the family would be tested for the KCNE1 mutation and have ongoing evaluation for both ARVC and LQTS. The proband will continue to be managed according to his clinical phenotype of ARVC as well as be informed of simple measures of avoiding QT-prolonging drugs. This scenario highlights the challenges of finding multiple DNA variants in cardiac genes and the key role of comprehensive phenotyping of patients and their at-risk relatives.
Illustrative cases
Case 3
While these are complex scenarios best dealt with on a caseby-case basis by centers with expertise in cardiac genetics,44 the following illustrative cases highlight some key principles in the evaluation of genetic findings in the clinical context.
A family presented to a specialized cardiac genetic service after the identification of a VUS in AKAP9 (LQTS11), an incidental finding from clinical exome testing performed to clarify the genetic cause of a neurological hereditary chorea in the family. The family underwent comprehensive cardiac assessment, and no members were found to have any evidence of LQTS. After discussion with the family, they were reassured that the AKAP9 variant is unlikely to be of clinical importance and no further investigation was recommended. This case highlights the emerging issue of “incidental findings,” particularly in the setting of clinical exome or genome testing. Again, detailed clinical phenotyping is critical in the interpretation of incidental findings.
Case 1 A 45-year-old man presented with a clinical diagnosis of mild HCM with a left ventricular wall thickness of 15 mm and a family history of SCD of his father aged 30 years. Commercial genetic testing of a “panel” of 10 HCM genes was performed and a novel variant Ile1160Fs MYBPC3 identified. This variant causes a novel insertion resulting in a frameshift likely leading to a loss of function of the protein, which provides additional support for disease causation. However, it was never reported before the testing laboratory reported it as “probably disease associated” and cautioned that it should not be used for predictive genetic testing unless coinheritance can be established. Fortunately, the proband’s first cousin was known to be clinically affected and willing to provide a DNA sample after discussion with the cardiac genetic counselor. The variant was subsequently confirmed in the cousin, and although there is a small chance that cosegregation occurred by chance, taking into consideration the strong functional evidence, the pathogenicity status was upgraded to allow testing of the family. Cosegregation of the genetic variant with disease in the context of a family is a key factor in determining pathogenicity.
Case 2 A 30-year-old man presented with a clinical diagnosis of ARVC based on 2010 task force criteria45 after a resuscitated cardiac arrest. Full cardiac evaluation did not reveal any additional findings, including a normal corrected QT interval (415 ms). A detailed family history revealed no history of cardiac disease or SCD, and this was confirmed after clinical screening of his sibling and parents, which included cardiac magnetic resonance imaging. The proband underwent a “chip-based” cardiac genetic test (approximately 60 cardiac genes), and a “likely pathogenic” mutation in KCNE1 Asp76Asn (LQT5) and a VUS in DSP Arg1537Cys (ARVC) were identified. The KCNE1 mutation has previously been
Future challenges The role of the cardiac genetic counselor as the interface between this complex genetic information and the families is increasingly important, particularly in the setting of pretest genetic counseling, where the goal is to ensure patients and their families are fully equipped and informed to make the best decision for their circumstances. Of equal importance is the role of the cardiologist in ensuring comprehensive phenotyping of the proband and clinical evaluation of firstdegree relatives before genetic testing. The multidisciplinary approach incorporating genetic counseling, cardiology, and expertise from many other fields is therefore the ideal model to deliver care. This is an area that will only continue to expand, both in accessibility to the wider disease population and in the number of genetic variants requiring interpretation. Furthermore, as continued research efforts shed light on the effect of gene modifiers, the potential for clinicians to better predict outcomes through genetics may be within reach. While targeted gene approaches may be a simpler solution, the reality is that large gene chip-based tests, clinical exome sequencing, and WGS are here. As we struggle to understand what this wealth of information means to cardiac genetic disease states in a clinical setting, from a research perspective the possibilities are endless. Despite the uncertainty and issues, it cannot be underestimated how incredibly powerful
1078 a genetic diagnosis can be for these families if carried out appropriately. Seamless collaboration and communication within the multidisciplinary team, including the cardiologist, genetic counselor, clinical geneticist, commercial testing center, and research laboratories will be the key to ensuring probabilistic genetic results are correctly conveyed, facilitating the effective and high-quality care of families with cardiac genetic diseases.
References 1. Sturm AC, Hershberger RE. Genetic testing in cardiovascular medicine: current landscape and future horizons. Curr Opin Cardiol 2013;28:317–325. 2. Das KJ, Ingles J, Bagnall RD, Semsarian C. Determining pathogenicity of genetic variants in hypertrophic cardiomyopathy: importance of periodic reassessment. Genet Med 2013;16(4):286–293. 3. Ackerman MJ, Priori SG, Willems S, et al. HRS/EHRA expert consensus statement on the state of genetic testing for the channelopathies and cardiomyopathies this document was developed as a partnership between the Heart Rhythm Society (HRS) and the European Heart Rhythm Association (EHRA). Heart Rhythm 2011;8:1308–1339. 4. Maron BJ, Maron MS, Semsarian C. Double or compound sarcomere mutations in hypertrophic cardiomyopathy: a potential link to sudden death in the absence of conventional risk factors. Heart Rhythm 2012;9:57–63. 5. Ingles J, Doolan A, Chiu C, Seidman J, Seidman C, Semsarian C. Compound and double mutations in patients with hypertrophic cardiomyopathy: implications for genetic testing and counselling. J Med Genet 2005;42:e59. 6. Bauce B, Nava A, Beffagna G, et al. Multiple mutations in desmosomal proteins encoding genes in arrhythmogenic right ventricular cardiomyopathy/dysplasia. Heart Rhythm 2010;7:22–29. 7. Kelly M, Semsarian C. Multiple mutations in genetic cardiovascular disease: a marker of disease severity? Circ Cardiovasc Genet 2009;2:182–190. 8. Girolami F, Ho CY, Semsarian C, Baldi M, Will ML, Baldini K, Torricelli F, Yeates L, Cecchi F, Ackerman MJ, Olivotto I. Clinical features and outcome of hypertrophic cardiomyopathy associated with triple sarcomere protein gene mutations. J Am Coll Cardiol 2010;55:1444–1453. 9. Schwartz PJ, Priori SG, Spazzolini C, et al. Genotype-phenotype correlation in the long-QT syndrome: gene-specific triggers for life-threatening arrhythmias. Circulation 2001;103:89–95. 10. Kapplinger J, Tester DJ, Ackerman MJ. The compounding dilemma of genetic noise: identification of the genetic noise rate in genes associated with cardiac channelopathies. Heart Rhythm 2013;10:1752–1753. 11. Jabbari J, Jabbari R, Nielsen MW, Holst AG, Nielsen JB, Haunso S, Tfelt-Hansen J, Svendsen JH, Olesen MS. New exome data question the pathogenicity of genetic variants previously associated with catecholaminergic polymorphic ventricular tachycardia. Circ Cardiovasc Genet 2013;6:481–489. 12. Andreasen C, Nielsen JB, Refsgaard L, Holst AG, Christensen AH, Andreasen L, Sajadieh A, Haunso S, Svendsen JH, Olesen MS. New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants. Eur J Hum Genet 2013;21:918–928. 13. Maron BJ, Maron MS, Semsarian C. Genetics of hypertrophic cardiomyopathy after 20 years: clinical perspectives. J Am Coll Cardiol 2012;60:705–715. 14. Pan S, Caleshu CA, Dunn KE, Foti MJ, Moran MK, Soyinka O, Ashley EA. Cardiac structural and sarcomere genes associated with cardiomyopathy exhibit marked intolerance of genetic variation. Circ Cardiovasc Genet 2012;5:602–610. 15. Tennessen JA, Bigham AW, O’Connor TD, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012;337:64–69. 16. Marian AJ. Causality in genetics: the gradient of genetic effects and back to koch postulates of causality. Circ Res 2014;114:e18–e21. 17. Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG. Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet 2013;6:337–346. 18. Ohanian M, Otway R, Fatkin D. Heuristic methods for finding pathogenic variants in gene coding sequences. J Am Heart Assoc 2012;1:e002642. 19. Hofman N, Tan HL, Alders M, Kolder I, de Haij S, Mannens MM, Lombardi MP, Dit Deprez RH, van Langen I, Wilde AA. Yield of molecular and clinical testing for arrhythmia syndromes: report of 15 years’ experience. Circulation 2013;128: 1513–1521. 20. Ingles J, Sarina T, Yeates L, Hunt L, Macciocca I, McCormack L, Winship I, McGaughran J, Atherton J, Semsarian C. Clinical predictors of genetic
Heart Rhythm, Vol 11, No 6, June 2014
21.
22. 23. 24.
25.
26.
27.
28.
29.
30.
31.
32.
33. 34. 35.
36. 37.
38.
39.
40.
41.
42.
43.
44. 45.
testing outcomes in hypertrophic cardiomyopathy. Genet Med 2013;15(12): 972–977. Gruner C, Ivanov J, Care M, Williams L, Moravsky G, Yang H, Laczay B, Siminovitch K, Woo A, Rakowski H. Toronto hypertrophic cardiomyopathy genotype score for prediction of a positive genotype in hypertrophic cardiomyopathy. Circ Cardiovasc Genet 2013;6:19–26. Ingles J, Yeates L, Semsarian C. The emerging role of the cardiac genetic counselor. Heart Rhythm 2011;8:1958–1962. Biesecker B. Goals of genetic counselling. Clin Genet 2001;60:323–330. Resta R, Biesecker BB, Bennett RL, Blum S, Hahn SE, Strecker MN, Williams JL. A new definition of genetic counseling: National Society of Genetic Counselors’ Task Force report. J. Genet Counsel 2006;15:77–83. Christiaans I, van Langen IM, Birnie E, Bonsel GJ, Wilde AA, Smets EM. Quality of life and psychological distress in hypertrophic cardiomyopathy mutation carriers: a cross-sectional cohort study. Am J Med Genet A 2009;149A:602–612. Ormondroyd E, Oates S, Parker M, Blair E, Watkins H. Pre-symptomatic genetic testing for inherited cardiac conditions: a qualitative exploration of psychosocial and ethical implications. Eur J Hum Genet 2013;22(1):88–93. Ingles J, Yeates L, Hunt L, McGaughran J, Scuffham PA, Atherton J, Semsarian C. Health status of cardiac genetic disease patients and their at-risk relatives. Int J Cardiol 2013;165:448–453. Yeates L, Hunt L, Saleh M, Semsarian C, Ingles J. Poor psychological wellbeing particularly in mothers following sudden cardiac death in the young. Eur J Cardiovasc Nurs 2013;12:484–491. Ingles J, Sarina T, Kasparian N, Semsarian C. Psychological wellbeing and posttraumatic stress associated with implantable cardioverter defibrillator therapy in young adults with genetic heart disease. Int J Cardiol 2013;168:3779–3784. James CA, Tichnell C, Murray B, Daly A, Sears SF, Calkins H. General and disease-specific psychosocial adjustment in patients with arrhythmogenic right ventricular dysplasia/cardiomyopathy with implantable cardioverter defibrillators: a large cohort study. Circ Cardiovasc Genet 2012;5:18–24. Ingles J, Yeates L, O’Brien L, McGaughran J, Scuffham PA, Atherton J, Semsarian C. Genetic testing for inherited heart diseases: longitudinal impact on health-related quality of life. Genet Med 2012; Epub May 3. Christiaans I, van Langen IM, Birnie E, Bonsel GJ, Wilde AA, Smets EM. Genetic counseling and cardiac care in predictively tested hypertrophic cardiomyopathy mutation carriers: the patients’ perspective. Am J Med Genet A 2009;149A:1444–1451. Aatre RD, Day SM. Psychological issues in genetic testing for inherited cardiovascular diseases. Circ Cardiovasc Genet 2011;4:81–90. Green RC, Lupski JR, Biesecker LG. Reporting genomic sequencing results to ordering clinicians: incidental, but not exceptional. JAMA 2013;310:365–366. Green RC, Berg JS, Grody WW, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013; 15:565–574. Grove ME, Wolpert MN, Cho MK, Lee SS, Ormond KE. Views of genetics health professionals on the return of genomic results. J Genet Counsel 2013;Epub June 2. Bezzina CR, Barc J, Mizusawa Y, et al. Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death. Nat Genet 2013;45:1044–1049. Crotti L, Monti MC, Insolia R, Peljto A, Goosen A, Brink PA, Greenberg DA, Schwartz PJ, George AL Jr. NOS1AP is a genetic modifier of the long-QT syndrome. Circulation 2009;120:1657–1663. Crotti L, Hu D, Barajas-Martinez H, et al. Torsades de pointes following acute myocardial infarction: evidence for a deadly link with a common genetic variant. Heart Rhythm 2012;9:1104–1112. Hu D, Barajas-Martinez H, Medeiros-Domingo A, et al. A novel rare variant in SCN1Bb linked to Brugada syndrome and SIDS by combined modulation of Na (v)1.5 and K(v)4.3 channel currents. Heart Rhythm 2012;9:760–769. Ploski R, Pollak A, Muller S, Franaszczyk M, Michalak E, Kosinska J, Stawinski P, Spiewak M, Seggewiss H, Bilinska ZT. Does p.Q247X in TRIM63 cause human hypertrophic cardiomyopathy? Circ Res 2014;114:e2–e5. Appelbaum PS, Waldman CR, Fyer A, Klitzman R, Parens E, Martinez J, Price WN II, Chung WK. Informed consent for return of incidental findings in genomic research. Genet Med 2013; Epub Oct 24. Klitzman R, Buquez B, Appelbaum PS, Fyer A, Chung WK. Processes and factors involved in decisions regarding return of incidental genomic findings in research. Genet Med 2013; 16(4):311–317. Caleshu C, Day S, Rehm HL, Baxter S. Use and interpretation of genetic tests in cardiovascular genetics. Heart 2010;96:1669–1675. Marcus FI, McKenna WJ, Sherrill D, et al. Diagnosis of arrhythmogenic right ventricular cardiomyopathy/dysplasia: proposed modification of the task force criteria. Circulation 2010;121:1533–1541.