Clinical utility gene card for: Long-QT syndrome

#192500 (LQT1, KCNQ1-LQTS) #613688 (LQT2, KCNH2-LQTS) #603830 (LQT3, SCN5A-LQTS) #600919 (LQT4, ANK2-LQTS) #613695 (LQT5, KCNE1-LQTS) #613693 (LQT6, KCNE2-LQTS) #170390 (LQT7), (KCNJ2-)Andersen-Tawil syndrome #601005, 618447 (LQT8), (CACNA1C-)Timothy syndrome #611818 (LQT9, CAV3-LQTS) #611819 (LQT10, SCN4B-LQTS) #611820 (LQT11, AKAP9-LQTS) #612955 (LQT12, SNTA1-LQTS) #613485 (LQT13, KCNJ5-LQTS) #616247 (LQT14, CALM1-LQTS) #616249 (LQT15, CALM2-LQTS) #114183 (LQT16, CALM3-LQTS) n.a. (LQT 17, TRDN-LQTS) #220400 JERVELL AND LANGE-NIELSEN SYNDROME 1; JLNS1 #612347 JERVELL AND LANGE-NIELSEN SYNDROME 2; JLNS2

Comment: It may be appropriate to limit the use of numbered LQTS to LQTS 1-3 and the remaining to their pathogenic basis, such as CALM-LQTS rather than LQT14 [1].

Mutational spectrum
Out of the 17 genes reported to be associated with LQTS, 3 genes (KCNQ1, KCNH2, SCN5A) are classified having definitive evidence as a genetic cause for LQTS. In more than 90% of the positive LQTS cases a variant affecting function is found in these three core genes. In addition, CALM1, CALM2, CALM3 and TRDN have a definitive or strong evidence for disease causation, but are associated with specific features. For variants affecting function in the three CALM genes, LQTS may present during infancy or early childhood with heart block and severe QT prolongation. At least 30% of patients with clinical clear LQTS are genotype elusive. Common variations likely contribute to phenotype in cases without a known Mendelian variant, but it is likely that there are other genetic and non-genetic factors involved [2].
Cases with TRDN mutations presented during early childhood with QT prolongation, negative T waves in precordial leads and exercise-induced arrhythmia related to homozygous or compound heterozygous disease-associated variants. Cases with biallelic loss-of-function variants in TRDN can present with either a CPVT or LQTS-like phenotype. Prolonged QTc is not always observed. In cases where it is, it can be classified as atypical LQTS but this is not always the case. The gene CACNA1C was reported to have a moderate evidence for disease causation in the absence of multiorgan involvement as in Timothy syndrome. The level of evidence for the gene KCNJ2 was only limited for the cardio-specific phenotype of LQTS, whereas both genes (CACNA1C and KCNJ2) were classified to have definitive evidence for causing multiorgan syndromes (respectively: Timothy syndrome and Andersen-Tawil syndrome). Timothy syndrome might be associated with distinctive facial features, developmental delay, endocrine abnormalities and congenital heart defects besides bradycardia, QT prolongation and polymorphic arrhythmias [3]. Extracardiac manifestations of Andersen-Tawil syndrome may present as hypo-or hypercalemic episodes of paralysis (periodic paralysis) and morphological characteristics as low set ears, clinodactyly or hypertelorism. Andersen-Tawil syndrome is still classified as LQTS although prominent U waves tempted to determine a prolonged QT interval due to inclusion of the U wave [4].
The spectrum of disease-associated variants (of the loss-offunction subtypes) contains practically all types of variants affecting function (missense, nonsense, splice site, deletions and insertions). Most patients are heterozygous for a variant affecting function, but in~5% of the cases, patients carry two disease-associated variants in the same or different genes.

Analytical validation
Sequencing of all coding exons and intron-exon boundaries of the eligible genes as listed above. Analysis can be performed by Sanger sequencing, (as part of a (cardio) defined gene  Sequencing by the Sanger method is predicted to detect >99% of variants in the target regions. Sequencing of both strands (forward and reverse) is recommended. An independent analysis of a second sample of the patient is warranted.
Using NGS as the sequencing method, the sensitivity will depend on the characteristics of test, including (sequencing strategy (e.g. panel/exome/genome), enrichment method), coverage of target regions, base quality and read depth.
Classification of detected variants should be performed according to published standards (e.g. standards of the American College of Medical Genetics and Genomics (ACMG) [5] and should be used with customisation for the specific features of LQTS and its associated genes.
1.6 Estimated frequency of the disease (Incidence at birth ('birth prevalence') or population prevalence. If known to be variable between ethnic groups, please report): 1:2,000 in the general population. It may be assumed that the prevalence is of comparable magnitude in different populations [6].

Diagnostic setting
Comments: Comment 1: Prenatal diagnosis of Long-QT syndrome is indicated in very exceptional situations only and is asked for extremely rarely.
Comment 2: Among clinically definite LQTS cases the three most frequently affected genes with a disease-causing change are KCNQ1, KCNH2 and SCN5A. Most of the LQTS patients are heterozygous for a variant affecting function, but in~5% of the cases, patients carry two variants affecting function in the same gene (compound heterozygous or homozygous), or in different genes (digenic) [7,8]. In general, this is associated with a more severe phenotype with younger age of onset and more adverse events, suggesting a gene-dosage effect. Comment 3: Copy number variation might be present in 3-12% of patients in core genes [9][10][11][12][13].  Presenting with negative T waves in precordial leads, and exercise-induced arrhythmias in early childhood related to homozygous or compound heterozygous frameshift mutations.

if tested by conventional Sanger sequencing
Close to 100% if complete Sanger sequencing and deletion/ duplication (MLPA) analysis of the affected clinically important regions of each gene is performed. MLPA is indicated for KCNQ1, KCNH2 and KCNJ2. In SCN5A there is insufficient evidence for CNV causing a gain-of-function. But this nearly 100% analytical sensitivity includes variants affecting function as well as variants that are just innocent bystanders where the clinical impact has to be proven subsequently. Potential non-coding pathogenic variants in the 3 core genes may remain undetected by standard sequencing approaches, e.g. deep intronic splice variants.

if tested by Next-generation sequencing
Analytical sensitivity for single nucleotide variants, insertions and deletions: >99% at ≥50× read depth if MLPA and bioinformatic copy number variation (CNV) analysis is included (targeted next-generation sequencing panel approach) [14].
Lack of coverage of specific target regions is a common problem of all NGS platforms. In some cases, the problem can be particularly relevant. For example, some exons of KCNH2 are frequently not completely covered due to their high CG-rich sequence. Thus, additional analysis by Sanger sequencing of these uncovered regions is often required [15,16]. Core genes (KCNQ1, KCNH2, SCN5A) including flanking splice sites should be entirely and sufficiently covered (at least 20x). Potential non-coding pathogenic variants in the 3 main genes may remain undetected by standard sequencing approaches, e.g. deep intronic splice variants.

Analytical specificity
(proportion of negative tests if the genotype is not present)

if tested by conventional Sanger sequencing
Close to 100% if complete sequencing and MLPA of the affected gene is performed. But not finding a diseaseassociated variant rejects by no means the diagnosis LQTS in definite clinical cases as in about 30% the underlying cause or causative genes are still not known.

Clinical sensitivity (proportion of positive tests if the disease is present)
The clinical sensitivity can be dependent on variable factors such as age or family history. In such cases, a general statement should be given, even if a quantification can only be made case by case.

if tested by conventional Sanger sequencing
On average the detection rate of variants affecting function for the most frequent LQTS disease genes (KCNQ1, KCNH2, and SCN5A) is about 60-70% [17].

if tested by next-generation sequencing
Extra sensitivity due to sequencing additional genes by NGS is minimally higher as each additionally tested gene mentioned in table a.1.3.1 and 1.4 increases sensitivity slightly.

Clinical specificity (proportion of negative tests if the disease is not present)
The clinical specificity can be dependent on variable factors such as age or family history. For instance, some patients show an incomplete phenotype, in some individuals the diagnosis is established in adulthood, because of a late onset of symptoms. These cases can likely result in a lower sensitivity. In such cases, a general statement should be given, even if a quantification can only be made case by case.

if tested by conventional Sanger sequencing
About 95%, however, the rate of rare variants of uncertain significance (i.e. non-synonymous genetic variation) in Caucasians is about 4-8% in Non-Caucasian in the LQTS 1-3 genes [18].

Positive clinical predictive value (life time risk to develop the disease if the test is positive)
Before the age of 40 years roughly 40% of (untreated) patients with LQTS1 and LQTS2 become symptomatic. In LQTS3 this is less, but symptoms may be more severe. Phenotypic expression of the disorder is time-dependent and LQTS subjects maintain a high risk for life-threatening cardiac events after age 40 years, which seems to be less high for LQTS1 [19,20].

Negative clinical predictive value (Probability not to develop the disease if the test is negative)
(Probability not to develop the disease if the test is negative).
Assume an increased risk based on family history for a non-affected person. Allelic and locus heterogeneity may need to be considered.
Index case in that family had been tested: If the index case in that family had been tested and a non-equivocal disease-associated variant had been found in the index patient and the non-affected proband is not a carrier of the identified disease-associated variant close to 100%. In those cases the risk remains as small as the prevalence of the disease in the general population.
Index case in that family had not been tested: If the patient is clinically affected (prolonged QTc with or without syncope) the index patient has a chance of about 60-70% carrying a variant affecting function. But only in very rare cases there is an indication for performing LQTS genetic testing in a clinically unaffected relative when the index case has not been tested.
This could be imaginable when in an index case there is a strong clinical suspicion of LQTS and there is no DNA available or the index patient refuses genetic testing. Usually, there is no indication for genetic testing in a clinically unaffected family member with unclear genetic status of the index patient if the ECG is normal.

Clinical Utility
3.1 (Differential) diagnostics: The tested person is clinically affected (To be answered if in 1.9 "A" was marked) 3

Describe the burden of alternative diagnostic methods to the patient
ECGs are a non-invasive procedure with no risks and little inconvenience for the patient. But for the reason of low sensitivity and specificity the burden is psychological: uncertainty of proper diagnosis as well as appropriate clinical care: individual therapy, individual recommendations for treatment, life style adaption and individual risk stratification based on specific subtype are not possible in the absence of a genetic substrate.

3.1.3
How is the cost effectiveness of alternative diagnostic methods to be judged?
As far as a disease-causing mutation is identified in the index patient, genetic testing can be offered to apparently healthy relatives within the family in order to determine if they carry the same variant affecting function and are at risk for malignant ventricular arrhythmias. If the relative carries the known disease-associated variant a prophylactic inexpensive medical treatment can be started and specific advice can be given to gene carriers (avoiding substances/drugs which might trigger arrhythmias, avoidance of genotype-specific triggers for arrhythmias, careful attendance in case of pregnancy and delivery, reproductive counselling, counselling concerning choice of profession). There is a reduction of the relative risk for developing serious cardiac events of about 65% by proper treatment (mostly with an inexpensive betablocker therapy) and the cardiac events in untreated patients on the other hand may lead to early invalidity or death in otherwise often healthy young people with putative high economic loss.

Will disease management be influenced by the result of a genetic test?
No. □

Therapy (please describe)
Pharmaceutical treatment (usually beta-blockers) as primary and secondary prevention. In rare individual cases additional pacemaker and/or an implantable cardioverter defibrillator (ICD), and/ or left cardiac sympathetic denervation (LCSD) is used. The implantation of an ICD with or without the performance of LCSD is mostly reserved for patients in which optimal non-invasive therapy and lifestyle modifications fail to protect against ventricular arrhythmias. Only in exceptional individual cases ICD implantation might be indicated for primary prevention. For more specific therapeutic recommendations please see [22]. Pharmacotherapy might differ between genotypes. Also, life style advices are different for the different genotypes [23,24].
Prognosis (please describe) In general, even in asymptomatic subjects carrying the disease associated variant, regular preventive medical check-ups to recognise disease progression early, and appropriate treatment improve prognosis. On appropriate treatment and with appropriate life style adjustments prognosis is good in the vast majority of patients and may not differ from normal [25,26].

Management (please describe)
Regular preventive medical consultation of carriers of a variant affecting function, adjustment or intensification of therapy if appropriate (including defibrillator implantation and/or LCSD), if necessary.
The molecular-genetic information is very important for counselling and clinical management related to the different subtypes of the disease.
3.2 Predictive setting: the tested person is clinically unaffected but carries an increased risk based on family history (To be answered if in 1.9 "B" was marked)
Some disease associate variants have an unusually high clinical severity (e.g., KCNQ1 A341V) [9]. Also patients with compound heterozygous variants affecting function and JLNS patients are at a higher risk.
If the test result is negative (please describe): Precautionary measures as described above are not needed.

Which options in view of lifestyle and prevention does a person at-risk have if no genetic test has been done (please describe)?
Same as described above. However, the preventive measures are much better accepted and compliance is improved if a positive test result was obtained.

Genetic risk assessment in family members of a diseased person
(To be answered if in 1.9 'C' was marked)

Does the result of a genetic test resolve the genetic situation in that family?
If a disease-associated variant is found: yes. Otherwise, potentially affected relatives should undergo regular cardiologic evaluation.

Can a genetic test in the index patient save genetic or other tests in family members?
No. But in case of a positive test result in the index patient, clinically asymptomatic relatives being non-carriers of the disease associate variant can be excluded from regular cardiologic follow-up.

Does a positive genetic test result in the index patient enable a predictive test in a family member?
No. But it enables a diagnostic test in family members with a normal ECG (~40% of individuals carrying a variant affecting function).

Prenatal diagnosis
(To be answered if in 1.9 'D' was marked)

Does a positive genetic test result in the index patient enable a prenatal diagnosis?
Yes, but prenatal diagnostics are not actively offered.

If applicable, further consequences of testing
Please assume that the result of a genetic test has no immediate medical consequences. Is there any evidence that a genetic test is nevertheless useful for the patient or his/her relatives? (Please describe) For every patient (clinically affected or not) there are known specific triggers for arrhythmias to be avoided (e.g. QT prolonging drugs, competitive sports, low potassium serum levels, swimming in LQTS1, sudden loud noise in LQTS2) [7,8,23,24]. Thus, there should be thorough counselling concerning lifestyle modifications and choice of employment.
This work was supported by EuroGentest2 (Unit 2: 'Genetic testing as part of health care'), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics.
Funding Open Access funding enabled and organized by Projekt DEAL.

Compliance with ethical standards
Conflict of interest The authors declare no competing interest.
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