Long QT Panel, Sequencing and Deletion/Duplication

  • Use to confirm diagnosis of LQTS in symptomatic individuals
  • Use for presymptomatic testing in individuals with family history of LQTS or sudden cardiac death

Preferred test to assess for hereditary form of cardiomyopathy or arrhythmia

  • Assess for a familial sequence variant previously identified in a family member.
  • A copy of the relative's genetic laboratory report documenting the familial variant is required.

Long QT syndrome (LQTS) is characterized by prolongation of the QTc interval and T-wave abnormalities on an electrocardiogram (ECG) in the absence of specific conditions known to lengthen it, such as QT-prolonging drugs. LQTS is associated with tachyarrhythmias, often torsade de pointes (TdP), which may result in syncope, ventricular fibrillation, or sudden cardiac death. Cardiac events may occur from infancy to middle age but are most common in preteens and young adults. Common triggers for cardiac events include exercise, loud noises, emotional stress, or sleep. Not all individuals with a pathogenic variant in an LQTS-associated gene have ECG abnormalities or cardiac symptoms. Syndromic forms of LQTS associated with additional noncardiac features include Andersen-Tawil syndrome, Timothy syndrome, and Jervell and Lange-Nielsen syndrome (JLNS). Molecular confirmation of LQTS in symptomatic individuals or at-risk family members is useful to initiate treatment to prevent syncope or sudden death.

Disease Overview

Clinical Findings

  • Syncope
  • Cardiac arrest/sudden cardiac death
  • ECG abnormalities
    • Prolonged QTc interval on ECG
    • Torsade de pointes
    • T wave alternans
    • Notched T wave
    • Low heart rate for age
  • Syndromic forms of LQTS:
    • Andersen-Tawil syndrome
      • Characteristic facial features
      • Periodic paralysis/muscle weakness
    • Timothy syndrome
      • Characteristic facial features
      • Cutaneous syndactyly of hands/feet
      • Neurodevelopmental disorder
    • JLNS
      • Congenital sensorineural hearing loss

Genetics

Genes

Sequencing and deletion/duplication: CACNA1C, CALM1, CALM2, CALM3KCNE1, KCNE2, KCNH2, KCNJ2, KCNQ1, SCN5A, TRDN

Etiology

Pathogenic germline variants in genes associated with LQTS 

Commonly implicated genes with estimated contribution to congenital LQTS:

  • KCNQ1 (30-35%)
  • KCNH2 (25-30%)
  • SCN5A (5-10%)

Penetrance

Variable, influenced by gene involved

Of individuals with a pathogenic variant in an LQTS-associated gene:

  • An estimated 25% do not show QTc prolongation on ECG
  • Approximately 50% or less have clinical symptoms

Prevalence

1/2,500 for congenital LQTS

Inheritance

Typically, autosomal dominant with incomplete penetrance

Autosomal recessive inheritance for JLNS

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Clinical Sensitivity

60-75% 

Analytic Sensitivity

For massively parallel sequencing:

Variant Class Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region Analytic Specificity (NPA)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [Single exon]

>99.9

Exon-levelc duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA).

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; PPA, positive percent agreement; NPA, negative percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude a heritable form of LQTS.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if this patient has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of targeted genes
    • Regulatory region and deep intronic variants
    • Breakpoints of large deletions/duplications
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by MPS
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Deletions/duplications less than 1kb in the targeted genes
    • Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
    • Low-level somatic variants
    • Single exon deletions/duplications in the following exons:
        •  
      • KCNH2 (NM_000238, NM_172056) 6
      • KCNH2 (NM_001204798, NM_172057) 2
      • TRDN (NM_006073, NM_001251987, NM_001256020, NM_001256021, NM_001256022) 5
      • CALM1 (NM_001363670) 1
    • Duplications in the following genes: CAV3, KCNE1, KCNE2

Genes Tested

Gene MIM # Associated Disorder(s) Inheritance

CACNA1C

114205

LQTS 8

Timothy syndrome

AD

CALM1

114180

LQTS 14

CPVT 4

AD

CALM2

114182

LQTS 15

AD

CALM3

114183

LQTS 16

AD

KCNE1

176261

JLNS2

AR

LQTS 5

AD

KCNE2

603796

Familial atrial fibrillation 4

LQTS 6

AD

KCNH2

152427

LQTS 2

SQTS 1

AD

KCNJ2

600681

Andersen-Tawil syndrome

SQTS 3

Familial atrial fibrillation 9

AD

KCNQ1

607542

Familial atrial fibrillation 3

SQTS 2

LQTS 1

AD

JLNS 1

AR

SCN5A

600163

Progressive/nonprogressive heart block

Brugada syndrome 1

Dilated cardiomyopathy 1E

Familial atrial fibrillation 10

Familial ventricular fibrillation 1

LQTS 3

AD

Sick sinus syndrome 1

AR

TRDN 603283 Cardiac arrhythmia syndrome, with or without skeletal muscle weakness AR

AD, autosomal dominant; AR, autosomal recessive; CPVT, catecholaminergic polymorphic ventricular tachycardia; SQTS, short QT syndrome

References