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Genetics
Use and interpretation of genetic tests in cardiovascular genetics
  1. Colleen Caleshu1,
  2. Sharlene Day2,
  3. Heidi L Rehm3,
  4. Samantha Baxter4
  1. 1Program in Cardiovascular Genetics, Division of Medical Genetics, University of California, San Francisco, California, USA
  2. 2Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Health System, Ann Arbor, Michigan, USA
  3. 3Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, USA
  4. 4Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, USA
  1. Correspondence to Colleen Caleshu, Stanford Center for Inherited Cardiovascular Disease, 300 Pasteur Dr Boswell, A201C Stanford, CA 94305-5233, USA; cobrown{at}stanfordmed.org

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Our understanding of the genetic basis of many Mendelian forms of cardiovascular disease has advanced significantly in the last 5–10 years. There are now many professional society guidelines that recommend genetic testing for a variety of hereditary cardiovascular diseases including long QT syndrome, hypertrophic cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy (ARVC).1–3 The number of genes associated with cardiac conditions continues to increase, and the number of clinically available genetic tests for cardiac conditions has expanded rapidly in recent years (table 1).

Table 1

Genetic tests for hereditary cardiac conditions. Genetic tests for hereditary cardiac conditions typically involve sequencing some or all of the various genes associated with a given condition. The number of genes included and the sequencing methodology used may vary by laboratory. Some laboratories also offer analyses to look for duplications or deletions in the associated genes

Clinical genetic testing can be highly valuable in the management of families with hereditary disease. Determining which family members inherited the genetic predisposition to cardiac disease allows us to separate those in need of lifelong clinical evaluations from those who need no further evaluations beyond those recommended for the general population. This strategy is particularly valuable in inherited cardiovascular diseases where definitive clinical diagnosis of at-risk relatives is limited by incomplete penetrance, variable age of onset and, in some cases, insensitivity of clinical testing.4–7

Recent guidelines and expert opinions have gone beyond simply recommending genetic testing; they emphasise important points for the judicious use of genetic testing such as performing genetic testing on the most clearly affected person in the family, careful genetic counselling regarding the implications of positive, negative or uncertain results, and consideration of referral to a specialised centre due to the complexity of such genetic evaluations.1 8 9 To further elucidate principles and approaches critical to the effective use of genetic tests, we present four cases evaluated in cardiovascular genetics clinics and laboratories that illustrate the importance of appropriate use and accurate interpretation of genetic tests.

Case 1

A 33-year-old woman with a clinical diagnosis and family history of dilated cardiomyopathy (DCM) presents for evaluation. The patient brings up concerns about her three children, all under the age of 10 years. She lost two brothers at young ages to sudden cardiac death and fears for the loss of her children. The clinician brings up the utility of genetic testing, and explains how the results of her test could be used to determine whether or not her children are at risk for developing DCM. The patient consents to genetic testing and has a sample sent to a clinical laboratory. The results come back inconclusive; the test identified a novel variant that is of unknown significance due to its absence from the literature and limited control information. All other known affected family members are deceased so segregation studies are not possible. The patient requests that her three young children are tested for the variant. Despite warning the patient that the results should not be used for clinical decisions due to the uncertainty of the variant's significance, the physician allows testing to proceed. The results show that two of the children carry the variant and one does not. Unknown to the clinician the patient uses this information to decide that her middle child, who does not carry the variant, will play football, while the other two children, who do carry the variant, will have their activity restricted.

Almost a year after the patient's results were first reported, the laboratory calls the physician to inform her that they have changed the variant classification to presumed benign. The variant was recently reported to be present in 4/416 control chromosomes. Therefore, this variant is very unlikely to be the cause of this patient's DCM. All of her first degree relatives, including her children, still have a 50% risk to carry the mutation that is the cause of her DCM.

One of the benefits of using molecular diagnostics in the clinical setting is its utility for screening asymptomatic family members. However, these results are only clinically relevant in the presence of a true positive result.w1 When an inconclusive result is received, further family testing should be limited to parents, for assessing de novo occurrence, and to affected individuals or obligate carriers to determine if the variant segregates with the phenotype. There is limited utility to testing clinically unaffected family members. Any individual who does undergo genetic testing for a variant of uncertain significance should be appropriately counselled that these results should not be used to make clinical care decisions and that it is possible the variant could be pathogenic or benign. In this case young children were tested in order to reduce the anxiety of the mother, who used this information for lifestyle modification decisions without her clinician's knowledge.

Case 2

A 48-year-old woman with arrhythmogenic right ventricular cardiomyopathy (ARVC) and her 25-year-old son presented for evaluation. The son had a normal clinical evaluation, including an ECG, signal averaged ECG, echocardiogram, and MRI. Both mother and son were enrolled in a research study that included sequencing of known ARVC genes. A few years later the managing team received notification that a variant in the PKP2 gene had been identified in the son. This variant had not been reported before. The son was counselled that because he carried this variant he had inherited the predisposition to ARVC. He was offered an implantable cardioverter defibrillator, but declined.

Several years later the research team notified the clinical team that the mother's sequencing of the known ARVC genes had found no variants, including the variant identified in the son. The son was brought back for genetic counselling and told that this variant was not the inherited basis for ARVC in his family since his mother did not carry the PKP2 variant found in him. He was counselled that he remained at 50% risk of having inherited the predisposition to ARVC and should continue to have clinical screening.

This case demonstrates the challenges that arise when trying to interpret genetic test results on an unaffected relative without knowing the genotype of the affected family member. The significance of the variant found in the son can only be determined with knowledge of the mother's genotype. This underscores the prudence of starting testing with an affected family member and illustrates the need for caution in interpreting test results on an unaffected family member when the genotypes of affected family members are not known.

While sequencing on an unaffected relative found a variant of uncertain significance in this case, it could also have found no variants at all. That test result also provides no information about the individual's chances of developing the familial disease. This is because a negative result could indicate either that the disease-causing variant could not be identified or that the unaffected relative did not inherit the disease-causing variant. Unfortunately, distinguishing between these two very different results is not possible when testing unaffected relatives.

Case 3

A neonate is admitted to the neonatal intensive care unit (NICU) due to failure to thrive and is diagnosed with congenital hypertrophic cardiomyopathy (HCM). The mother was diagnosed with HCM at the age of 19 years after fainting following a run. She has mild septal hypertrophy with minimal symptoms. The maternal grandfather was reported to have died suddenly at the age of 45 of a similar ‘heart condition’. The father was not available for questioning, but the mother reports that everyone in his family is healthy. The physician explains that genetic testing may be able to clarify if her and her son's disease are being caused by the same genetic variant. The mother consents to testing and her sample is sent to a clinical laboratory. After the mother was found to be heterozygous for a pathogenic variant in MYH7, the son was tested specifically for that same variant and was found to carry it. The physician explained that their disease was caused by the same genetic problem, and the differences in disease severity could be explained by variable expressivity. In addition, the physician discusses that all future pregnancies would be at a 50% risk for inheriting the variant.

Three years later the father presents to the physician's clinic because his brother was recently diagnosed with HCM and genetic testing revealed a pathogenic variant in MYBPC3. He wants to be tested for this variant. Father and son had testing and were both found to carry the same MYBPC3 variant. Thus the son carried both the variant in MYBPC3 and the variant in MYH7.

While this case represents a small percentage of the HCM population, it demonstrates some of the important nuances involved with providing genetic counselling for cardiomyopathy. Approximately 5% of HCM probands have two variants in either one or more of the sarcomere genes. The presence of two variants may lead to earlier onset and/or increased severity of disease. Although HCM does have variable expressivity, the degree of variability seen in this case is rare and warrants further investigation, particularly given the genetic counselling implications of finding two variants instead of just one.

This case illustrates the value in performing the first comprehensive, multi-gene sequencing test on the most severely affected family member, since that individual is the family member most likely to carry more than one pathogenic variant and only full testing (not variant specific testing) will be able to pick up both variants. It also demonstrates the importance of pursuing further genetic testing if initial results do not adequately explain the clinical picture.

Case 4

A 12-year-old boy was diagnosed with long QT syndrome after a cardiac evaluation revealed a corrected QT interval of 520 ms following a syncopal episode while running. He was referred to the cardiovascular genetics clinic for genetic counselling, genetic testing, and evaluation of his family members. Sequencing of the five most common long QT genes was performed but no variants were found. The family was counselled that current genetic testing could not help determine which family members were at risk for long QT syndrome and that they should continue to have clinical screening.

Two years later additional genetic testing for long QT syndrome became clinically available. This additional testing was designed to find large deletions or duplications, which are missed by sequencing.10 The boy was brought back for a follow-up appointment in the cardiovascular genetics clinic and this expanded test was ordered. The test found a deletion in the KCNQ1 gene spanning several exons. The family was counselled that this deletion was the pathogenic variant that caused his long QT syndrome. The boy's sister, mother, and father were offered predictive genetic testing for the deletion, which determined that his sister and mother do not carry the deletion, but his father does.

Currently, genetic tests for most hereditary cardiovascular diseases have incomplete sensitivity, either due to lack of inclusion of all genes or loci involved, or due to technical limitations of identifying all forms of genetic variation. As in this case, current generation genetic tests fail to find the causative variant in a significant proportion of cases. However, as our knowledge of the genetic basis of cardiovascular disorders expands and genetic testing technology improves, expanded panels and new test modalities add to our ability to identify pathogenic variants in affected individuals. As illustrated by this case, patients who have had testing that did not identify a pathogenic variant may benefit from additional testing as it becomes available.

Discussion

In order to harness the clinical benefits of genetic tests and avoid the potential harms of misuse or misinterpretation of such tests, it is critical that the clinician consider carefully how best to use genetic tests to help a given family or patient. These cases illustrate ways to navigate several of the complexities and challenges of genetic testing.

Handling variants of unknown significance

Variants of unknown significance pose a challenge for genetic counselling in all areas of genetics. In cardiology, such variants are typically missense variants, lacking enough evidence to support pathogenicity, either due to a lack of control studies, presence in both affected and unaffected individuals at rare frequencies or their location within the gene. Familial segregation, protein function, species conservation and healthy control studies can all be used to argue for or against pathogenicity.11 12 However, all of these have limitations and sometimes the significance of the variant remains unknown. The classification of a variant may change over time, so the clinician should check in with the laboratory periodically.

One of the main challenges when counselling about a variant of unknown significance is explaining the limited clinical utility to a family. Thorough pre-test counselling of the patient, which includes the possibility of an inconclusive result, can prepare the patient for this information; post-test, thorough counselling on the implications of a variant of unknown significance is also needed.1 8 9 Studies have shown a wide range of perceived risk in individuals who receive inconclusive genetic test results. Twenty four per cent of women who received an inconclusive BRCA1/2 result perceived their risk for having a genetic basis to their cancer as low or very low 1 month later.w1

Testing unaffected relatives for a variant of uncertain significance will not determine if the at-risk relative inherited the condition, since it is unknown whether the variant is the true cause of the disease. Testing unaffected relatives for a variant of unknown significance also will not provide any insight into the pathogenicity of the variant because reduced and age dependent penetrance makes it impossible to classify clinically unaffected individuals phenotypically. Although the mother in case 1 was counselled that the results for her children were uninformative, they still altered her own perception of her children's risk status. This demonstrates the potential negative impact of testing at-risk relatives for variants of uncertain significance.

In the absence of informative genetic test results, all first degree relatives should be assumed to be at 50% risk and standard clinical screening guidelines should be followed (figure 1). The consequences of misuse or misinterpretation of testing for an uncertain variant, either by the provider or the family, are potentially grave, particularly in the setting of cardiovascular genetics. These include inappropriately discharging individuals who are at risk for sudden cardiac death from screening or implanting defibrillators in unaffected individuals. There is no evidence to support the utility of testing the clinically unaffected family members for a variant of unknown significance.

Figure 1

Decision tree for performing genetic testing for families with inherited cardiovascular diseases.

Selecting the best person to start genetic testing with

Genetic testing should, whenever possible, start with an affected family member.1 13 w2 The likelihood of finding the causative variant in a clinically unaffected relative is significantly lower than in an affected family member. As demonstrated in case 2, the results on unaffected relatives are often uninterpretable without knowing the genotype of an affected relative. If testing a clinically unaffected relative finds no variant or a variant of uncertain significance, the test results provide no information about whether or not the at-risk relative inherited the cardiovascular disease in the family. The results of testing an unaffected relative are only informative if a variant that is known to cause disease is identified.

In addition to the potential for results to be uninformative, there are significant implications if testing on an unaffected relative is misinterpreted. When a clinically unaffected relative is found to carry a variant of unknown significance, there is a risk this will be interpreted as the relative having inherited the disease, as was seen in case 2. When genetic testing on an unaffected individual does not find a variant, the concern is that the provider or patient will falsely interpret this as evidence they did not inherit the condition.

Given these limitations and challenges, testing of unaffected relatives without knowledge of the affected relative's genotype should be avoided. There may be times where such testing is considered, particularly in families with no living affected relatives. If this testing strategy is pursued, it should be approached with caution and should ideally be handled by a specialised cardiovascular genetics team, with careful pre- and post-test genetic counselling regarding the limitations of this testing and the likelihood of uninformative test results.1

In cardiovascular genetics there is significant reason to opt for a testing strategy that not only starts with an affected relative, but with the most severely affected relative.1 8 This is because a significant subset of cases of many hereditary cardiovascular diseases are caused by multiple variants.14 Multiple variants, either in the same or different genes, have been reported in 5–10% of cases of HCM,15 long QT syndrome,w3 and ARVC.16 Patients with two disease-causing variants may be homozygotes (two identical variants in both copies of one gene), compound heterozygotes (two different variants in both copies of one gene), or a double heterozygote (two variants in two different genes). Individuals with two or more variants often have an earlier age of onset, as well as a more severe presentation and worse prognosis.14 If two variants are present in the same family, they are more likely to be identified together in the most severely affected family member.

It is important to note that many of these families show an incomplete dominant pattern of inheritance; there is a ‘dosage effect’, with carriers of just one variant being more mildly affected than carriers of two variants.14 w3–w5 This means that the inheritance pattern and the spectrum of clinical presentations are dramatically different in families with two variants compared to families with just one variant. This has critical counselling implications, as indicated by case 3. Instead of having a 50% chance of carrying a variant that predisposes to disease, the siblings of a patient with two variants in the same gene have a 75% chance of having at least one variant that puts them at risk.

To ensure accurate genetic counselling and appropriate screening recommendations, every effort should be made to identify all the variants that are present in the family. Choosing the most severely affected individual and testing them with a comprehensive panel that includes many or all of the major genes associated with the phenotype can help achieve this (table 1). If testing has already been done on a mildly affected family member or if targeted testing of only a few genes has been done, it may be wise to pursue testing with a comprehensive panel in an affected individual whose phenotype is unusually severe.

Further testing

Both our knowledge of genes associated with genetic disease and the technologies used in genetic testing tend to improve over time, often at a rapid rate. As demonstrated by case 4, when initial testing on a family does not yield a pathogenic variant, additional testing may be helpful in the future. Whenever current genetic testing is less than 100% sensitive, there is potential for testing sensitivity to increase as new genes are found or new testing modalities are applied to the genes already associated with the disorder. Such progress in testing yield has been seen in many genetic diseases; recent examples include hereditary breast and ovarian cancer,w6 cytogenetic abnormalities,w7 and, as represented by case 4, long QT syndrome.10 Thus, when initial testing on an affected individual fails to identify the underlying genetic aetiology for their condition, it may be appropriate for that individual to be tested again in the future when new testing that improves yield is available. It is important that patients are counselled that advances in genetic testing are likely and that they should check in with the clinical team every few years to see if new testing is available.w8

Value of genetic consultation

Genetic counsellors and geneticists at the laboratory performing genetic testing can be valuable resources to the managing clinical team.17 A discussion with the genetic testing laboratory before testing can often help clarify who and when to test and how to interpret results. Genetic counsellors are often the primary clinical contacts for the laboratory and can provide clinicians with updated information on the classification of variants, additional testing being offered, as well as resources for the patient.

Studies have found that individuals with hereditary cardiovascular diseases prefer specialised multidisciplinary clinics that include genetic counsellors, and that these patients have better psychological outcomes when evaluated in such clinics.18 w9 A survey of cardiologists' and geneticists' preferences regarding the division of tasks in cardiovascular genetics found that both groups prefer a collaborative approach.19 The majority of cardiologists surveyed felt that a geneticist should be solely responsible for, or collaboratively involved in, all aspects of the genetics evaluation, including ordering and interpretation of genetic testing, genetic counselling, and screening and predictive testing for asymptomatic relatives.

As emphasised by recent guidelines from the Heart Failure Society of America and highlighted by these cases, genetics evaluations for hereditary cardiovascular disease are best performed by providers with the skills, training, and time that the level of complexity in these cases demands.1 The managing cardiology team should consider consulting with a cardiovascular genetics group if they do not have a team member who can provide adequate genetic counselling, pedigree assessment, and interpretation of genetic test results. Such a consultation can supplement the patient's ongoing care, without interfering with the relationship the patient has with their primary cardiologist.

Management of cardiovascular genetic conditions

Complex cases such as these raise questions regarding how to manage family members who carry genetic variants or who are at 50% risk with their genetic status unknown. While these issues are important, they are outside the scope of this article; we refer the reader to relevant guidelines and recommendations.1 2 6 w10–w12

Genetic testing in cardiovascular genetics: key points

  • Testing should be offered with thorough pre-and post-test genetic counselling.

  • Geneticists and genetic counsellors at the genetic testing laboratory are valuable resources for ensuring the appropriate use and interpretation of gene tests.

  • Genetic testing tends to improve over time. If a patient had genetic testing previously and the causative variant was not found, it may be appropriate for them to be tested again when newer tests with a higher sensitivity are available.

Choosing which family member to start genetic testing with

  • Genetic testing should start with a comprehensive panel on a clearly affected family member.

  • Starting genetic testing with the most severely affected family member increases the likelihood of finding all pathogenic variants that are present in the family.

  • Testing an unaffected family member without knowing the affected relative's genotype often produces uninformative test results and can lead to false assumptions about risk for developing the condition.

Handling and interpretation of variants of unknown significance

  • Potential pathogenicity of variants of unknown significance should be confirmed through segregation studies when possible.

  • Segregation studies should focus on affected family members; due to reduced and age dependent penetrance, currently unaffected family members cannot be classified for purposes of segregation studies.

  • Other data that can help clarify pathogenicity include prevalence in ethnically matched controls, in vitro data (if available), conservation across species, and predictive software.

  • Variants of unknown significance should not be used to determine clinically unaffected family members' predisposition to inherited cardiovascular disease.

  • The status of variants of unknown significance is often resolved with time; check back with the laboratory periodically to find out if the variant has been reclassified to either benign or pathogenic.

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Acknowledgments

We gratefully acknowledge our colleagues who referred these patients for a genetics evaluation and members of our clinical teams who were involved in the evaluation of each of these cases. We thank Dr Robert Nussbaum for his input on an early version of this manuscript.

References

  1. Recently published guidelines from the Heart Failure Society of America outlining what genetic evaluations are appropriate for patients with cardiomyopathies and their families. Provides screening recommendations for mutation carriers and individuals at 50% risk of carrying a mutation.

  2. Guidelines from Heart Rhythm UK on indications for genetic testing in channelopathies and cardiomyopathies; emphasises the role of genetic testing in determining which family members are, and are not, at risk.

  3. Excellent recent perspective on the role of genetic testing and genetic counselling in cardiomyopathies, with a good review of cardiomyopathy genetics by phenotype.

  4. First report of deletions and duplications in long QT genes. In a sample of long QT patients with normal sequencing of long QT genes, 12% had a deletion or duplication, suggesting the need for further analysis in long QT patients who have had normal sequencing.

  5. Recommendations from the American College of Medical Geneticists on reporting and classification of sequence variants, including approaches to help determine the clinical significance of variants of uncertain significance.

  6. Excellent review of the prevalence and clinical significance of multiple mutations in various hereditary cardiac conditions.

  7. Meta-analysis of studies on sequencing of sarcomeric genes in HCM. Provides data on yield of genetic testing, prevalence of mutations in particular genes, and frequency of multiple mutations.

  8. Thorough recent review of the genetics of arrhythmogenic right ventricular cardiomyopathy.

  9. Case series demonstrating how consulting with the clinical genetics laboratory throughout the genetic testing process can help clinicians maximise the utility and benefit of genetic testing.

  10. Study noting that HCM patients who receive evaluations in specialised cardiovascular genetics clinics that include genetic counselling have better psychological outcomes, including better adjustment to their disease and less worry.

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Footnotes

  • Funding This work was supported by: SD - NIH grant 1R01 HL093338-01A1. CB—Private grant from the Deb Foundation.

  • Competing interests In compliance with EBAC/EACCME guidelines, all authors participating in Education in Heart have disclosed potential conflicts of interest that might cause a bias in the article. HLR and SB are employees of Partners Healthcare Center for Personalized Genetic Medicine.

  • Provenance and peer review Commissioned; not externally peer reviewed.

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