- Email: [email protected]
MY APPROACH to genetic testing in cardiology practice
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Available online at www.sciencedirect.com
www.elsevier.com/locate/tcm
MY APPROACH
MY APPROACH to genetic testing in cardiology practice
Matteo Vatta, PhD, FACMG The use of genetic testing in cardiology practice has gained increasing interest and momentum in the last several years thanks to the advent of massive parallel sequencing technology called Next-Generation Sequencing (NGS). However, even though the usefulness of genetic testing has been recognized for a long time, it has not made it into day-to-day operations in all cardiology practice yet. Here I will discuss the molecular diagnostic approach to patients with long QT syndrome (LQTS), for which genetic testing and counseling is a Class I indication, meaning that “evidence and/or general agreement that a given procedure or treatment is beneficial, useful, and effective.” As a clinical molecular geneticist, my approach to genetic testing begins after a comprehensive clinical evaluation by a cardiologist, usually followed by a clinical geneticist consult, when appropriate, and pretesting counseling by a genetic counselor. While a significant number of patients with LQTS exhibit a baseline ECG with distinctive patterns suggesting alterations in specific currents (such as LQT1, LQT2, LQT3), the precise underlying molecular defect can be identified only after performing comprehensive clinical genetic tests. Currently, defects in three genes (KCNQ1, KCNH2, and SCN5A) coding for the alpha subunits of two potassium channels and one sodium channel, respectively, cause approximately 75% of all LQTS cases. However, an additional 10 genes (AKAP9, ANK2, CACNA1C, CAV3, KCNE1, KCNE2, KCNJ2, KCNJ5, SCN4B, *
and SNTA1) have been linked to LQTS, covering cumulatively an extra 5% to 10% of cases. Moreover, copy number variant (CNV) due to large rearrangements affecting all LQTS genes can explain an additional handful of cases, thus suggesting that the genetic basis of the remaining 10% of cases is still unknown. Genetic testing for LQTS has become standard of care once the diagnosis has been made. It is well-known that genetic test results may support patient management. Individuals harboring a deleterious variant in KCNQ1 are more likely to respond well to beta-blocker therapy compared with variants in the other two genes (KCNQ14KCNH24SCN5A). Moreover, in symptomatic patients with deleterious variants in SCN5A, a permanent pacemaker and implantable cardioverter defibrillator (ICD) therapy should be considered. Although prolonged QTc interval and cardiac arrhythmias could represent the main findings in LQTS patients, they may also show evidence of additional clinical features such as, but not limited to, syndactyly, autism, facial dysmorphologies, scoliosis, and short stature, which could suggest more complex presentations, such as in Timothy syndrome caused by deleterious variants in CACNA1C, or Andersen–Tawil syndrome, associated with KCNJ2 variants. Moreover, it has been recently recognized that there is a link between LQTS and some forms of epilepsy. In all cases, recognizing non-cardiac features involving other medical services and detailing the clinical picture, along with in-depth past clinical and family history, greatly helps the interpretation of diagnostic laboratory tests and the pre- and post-test counseling of LQTS patients. This is particularly important provided the range of overlapping diseases caused by deleterious variants from a gene pool such as that associated with LQTS. Thus, opting for a panel of genes covering the majority of LQTS cases, and possibly including those genes associated with more complex presentations, as discussed above, represents the best strategy. Once, the specific test has been decided, there are three possible outcomes from the laboratory tests: negative, positive, and uncertain, which occurs when a “variant of uncertain clinical significance” (VUS) is detected. This basic
First published on PracticeUpdate on February 18, 2015. Republished with permission.
http://dx.doi.org/10.1016/j.tcm.2015.05.018 1050-1738/& 2016 Published by Elsevier Inc.
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classification encompasses an interpretation based on three major levels of evidence of pathogenicity such as: 1. Type of variant detected (ie, splicing, nonsense, frameshift, missense, non-frameshift, synonymous, gross alterations) and its position in the gene and protein, along with what is known about the underlying pathogenic mechanism (ie, haplo-insufficiency, gain of function, dominantnegative, etc) 2. Genetic studies performed (ie, extensive linkage data with LOD score 43 in a large multigenerational family or in multiple small multigenerational families in which the variants co-segregate with the disease in affected individuals or when the variant occurs de novo in the index case with no previous family history) 3. Functional studies performed (ie, in vitro, cellular model, animal model, etc) demonstrating a deleterious effect of the detected variant Although LQTS is regarded as a monogenic Mendelian disease, caused by one deleterious variant in one of the above-mentioned genes, up to 8% of patients harbor two or more deleterious
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variants, causing a more severe clinical presentation. Most functionally proven deleterious variants are unique to the proband and his/her family (“private” variant) or rare, but others, such as the KCNE1 p.D85N, can occur in approximately 0.8% of the general population. This suggests that some more common variants may have a known damaging effect, but they might not be sufficient in isolation to unveil an overt LQTS phenotype. Therefore, currently the interpretation of genetic tests is subjected to the complexity of the molecular basis of LQTS, and, even more than before, a comprehensive clinical approach along with pre- and post-genetic counseling is necessary to assess each variant effect and weight in the patient phenotype, as well as which variant(s) to be tested for in the proband's first-degree relatives to identify at-risk family members. Associate Professor of Medical and Molecular Genetics, Department of Medical and Molecular Genetics, Indiana University School of Medicine Associate Professor of Clinical Medicine, Department of Clinical Medicine, Indiana University School of Medicine E-mail address: [email protected]
E N D S I N
C
A R D I O V A S C U L A R
M
E D I C I N E
26 (2016) 97–98
Available online at www.sciencedirect.com
www.elsevier.com/locate/tcm
MY APPROACH
MY APPROACH to genetic testing in cardiology practice
Matteo Vatta, PhD, FACMG The use of genetic testing in cardiology practice has gained increasing interest and momentum in the last several years thanks to the advent of massive parallel sequencing technology called Next-Generation Sequencing (NGS). However, even though the usefulness of genetic testing has been recognized for a long time, it has not made it into day-to-day operations in all cardiology practice yet. Here I will discuss the molecular diagnostic approach to patients with long QT syndrome (LQTS), for which genetic testing and counseling is a Class I indication, meaning that “evidence and/or general agreement that a given procedure or treatment is beneficial, useful, and effective.” As a clinical molecular geneticist, my approach to genetic testing begins after a comprehensive clinical evaluation by a cardiologist, usually followed by a clinical geneticist consult, when appropriate, and pretesting counseling by a genetic counselor. While a significant number of patients with LQTS exhibit a baseline ECG with distinctive patterns suggesting alterations in specific currents (such as LQT1, LQT2, LQT3), the precise underlying molecular defect can be identified only after performing comprehensive clinical genetic tests. Currently, defects in three genes (KCNQ1, KCNH2, and SCN5A) coding for the alpha subunits of two potassium channels and one sodium channel, respectively, cause approximately 75% of all LQTS cases. However, an additional 10 genes (AKAP9, ANK2, CACNA1C, CAV3, KCNE1, KCNE2, KCNJ2, KCNJ5, SCN4B, *
and SNTA1) have been linked to LQTS, covering cumulatively an extra 5% to 10% of cases. Moreover, copy number variant (CNV) due to large rearrangements affecting all LQTS genes can explain an additional handful of cases, thus suggesting that the genetic basis of the remaining 10% of cases is still unknown. Genetic testing for LQTS has become standard of care once the diagnosis has been made. It is well-known that genetic test results may support patient management. Individuals harboring a deleterious variant in KCNQ1 are more likely to respond well to beta-blocker therapy compared with variants in the other two genes (KCNQ14KCNH24SCN5A). Moreover, in symptomatic patients with deleterious variants in SCN5A, a permanent pacemaker and implantable cardioverter defibrillator (ICD) therapy should be considered. Although prolonged QTc interval and cardiac arrhythmias could represent the main findings in LQTS patients, they may also show evidence of additional clinical features such as, but not limited to, syndactyly, autism, facial dysmorphologies, scoliosis, and short stature, which could suggest more complex presentations, such as in Timothy syndrome caused by deleterious variants in CACNA1C, or Andersen–Tawil syndrome, associated with KCNJ2 variants. Moreover, it has been recently recognized that there is a link between LQTS and some forms of epilepsy. In all cases, recognizing non-cardiac features involving other medical services and detailing the clinical picture, along with in-depth past clinical and family history, greatly helps the interpretation of diagnostic laboratory tests and the pre- and post-test counseling of LQTS patients. This is particularly important provided the range of overlapping diseases caused by deleterious variants from a gene pool such as that associated with LQTS. Thus, opting for a panel of genes covering the majority of LQTS cases, and possibly including those genes associated with more complex presentations, as discussed above, represents the best strategy. Once, the specific test has been decided, there are three possible outcomes from the laboratory tests: negative, positive, and uncertain, which occurs when a “variant of uncertain clinical significance” (VUS) is detected. This basic
First published on PracticeUpdate on February 18, 2015. Republished with permission.
http://dx.doi.org/10.1016/j.tcm.2015.05.018 1050-1738/& 2016 Published by Elsevier Inc.
98
TR
E N D S I N
C
A R D I O V A S C U L A R
classification encompasses an interpretation based on three major levels of evidence of pathogenicity such as: 1. Type of variant detected (ie, splicing, nonsense, frameshift, missense, non-frameshift, synonymous, gross alterations) and its position in the gene and protein, along with what is known about the underlying pathogenic mechanism (ie, haplo-insufficiency, gain of function, dominantnegative, etc) 2. Genetic studies performed (ie, extensive linkage data with LOD score 43 in a large multigenerational family or in multiple small multigenerational families in which the variants co-segregate with the disease in affected individuals or when the variant occurs de novo in the index case with no previous family history) 3. Functional studies performed (ie, in vitro, cellular model, animal model, etc) demonstrating a deleterious effect of the detected variant Although LQTS is regarded as a monogenic Mendelian disease, caused by one deleterious variant in one of the above-mentioned genes, up to 8% of patients harbor two or more deleterious
M
E D I C I N E
26 (2016) 97–98
variants, causing a more severe clinical presentation. Most functionally proven deleterious variants are unique to the proband and his/her family (“private” variant) or rare, but others, such as the KCNE1 p.D85N, can occur in approximately 0.8% of the general population. This suggests that some more common variants may have a known damaging effect, but they might not be sufficient in isolation to unveil an overt LQTS phenotype. Therefore, currently the interpretation of genetic tests is subjected to the complexity of the molecular basis of LQTS, and, even more than before, a comprehensive clinical approach along with pre- and post-genetic counseling is necessary to assess each variant effect and weight in the patient phenotype, as well as which variant(s) to be tested for in the proband's first-degree relatives to identify at-risk family members. Associate Professor of Medical and Molecular Genetics, Department of Medical and Molecular Genetics, Indiana University School of Medicine Associate Professor of Clinical Medicine, Department of Clinical Medicine, Indiana University School of Medicine E-mail address: [email protected]