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Long QT Syndrome Sequencing Panel

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits
TEST METHODS

Sequencing

Test Code TestCPT Code Copy CPT Codes
2601 AKAP9 81479 Add to Order
ANK2 81479
CACNA1C 81479
CALM1 81479
CALM2 81479
CAV3 81404
KCNE1 81479
KCNE2 81280
KCNH2 81406
KCNJ2 81403
KCNJ5 81479
KCNQ1 81406
SCN4B 81479
SCN5A 81407
SNTA1 81479
Full Panel Price* $1740.00
Test Code Test Total Price CPT Codes Copy CPT Codes
2601 Genes x (15) $1740.00 81280, 81403, 81404, 81406(x2), 81407, 81479(x9) Add to Order
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information. If you would like to order a subset of these genes contact us to discuss pricing.

For Sanger Sequencing click here.
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

It is estimated that this NGS panel can detect a pathogenic variant in approximately 80% of patients with LQTS (Splawski et al. 2000; Taggart et al 2007; Ackerman et al. 2011).

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Deletion/Duplication Testing via aCGH

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
600 AKAP9$690.00 81479 Add to Order
ANK2$690.00 81479
CACNA1C$690.00 81479
CAV3$690.00 81479
KCNE1$690.00 81479
KCNE2$690.00 81282
KCNH2$690.00 81479
KCNJ2$690.00 81479
KCNJ5$690.00 81479
KCNQ1$690.00 81479
SCN4B$690.00 81479
SCN5A$690.00 81479
SNTA1$690.00 81479
Full Panel Price* $1290.00
Test Code Test Total Price CPT Codes Copy CPT Codes
600 Genes x (13) $1290.00 81282, 81479(x12) Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

Gross deletions or duplications not detectable by Sanger sequencing have been reported in CAV3, KCNJ2 and SCN5A as individual cases but no statistical data is available yet (Human Gene Mutation Database). To date, no gross deletions or duplications have been reported in AKAP9, ANK2, CACNA1C, CALM1, CALM2, KCNE1, KCNE2, KCNJ5, SCN4B, and SNTA1  (Human Gene Mutation Database).

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Clinical Features

Long QT syndrome (LQTS) is a heritable channelopathy characterized by a prolonged cardiac repolarization that may trigger ventricular arrhythmias (torsade de pointes), recurrent syncopes, seizure, or sudden cardiac death (SCD) (Cerrone et al. 2012). LQTS can manifest with syncope and cardiac arrest that is commonly triggered by adrenergic stress, often precipitated by emotion or exercise. Roughly 10% to 15% of patients experience symptoms at rest or during the night (Schwartz et al. 2001). The mean age of onset of symptoms is 12 years, and earlier onset usually is associated with a more severe form of the disease (Priori et al 2004).

Genetics

Long QT syndrome, also known as Romano-Ward syndrome, is typically inherited in an autosomal dominant manner. Inherited LQTS occurs due to pathogenic variants in multiple genes. Up to 80% of autosomal dominant Long QT cases are due to heterozygous pathogenic variants in KCNQ1, KCNH2, and SCN5A (Ackerman et al. 2011). The remaining LQTS-associated genes account for less than 5% of total cases (Alders and Mannens 2015). See individual gene test descriptions for information on molecular biology of gene products. In addition to inherited forms, LQTS can also be acquired (acquired LQTS), usually as a result of pharmacological therapy. Long QT syndrome has an incidence of about 1 in 2500 individuals (Schwartz et al 2009).

Testing Strategy

For this Next Generation (NextGen) panel, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

All patients with symptoms suggestive of Long QT syndrome are candidates for this test.

Genes

Official Gene Symbol OMIM ID
AKAP9 604001
ANK2 106410
CACNA1C 114205
CALM1 114180
CALM2 114182
CAV3 601253
KCNE1 176261
KCNE2 603796
KCNH2 152427
KCNJ2 600681
KCNJ5 600734
KCNQ1 607542
SCN4B 608256
SCN5A 600163
SNTA1 601017
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Andersen-Tawil Syndrome/Long QT Syndrome via the KCNJ2 Gene
Brugada Syndrome 1 via the SCN5A Gene
Brugada Syndrome Sequencing Panel
Catecholaminergic Polymorphic Ventricular Tachycardia and Long QT Syndrome via the CALM1 Gene
Catecholaminergic Polymorphic Ventricular Tachycardia Sequencing Panel
Caveolinopathy via the CAV3 Gene
Comprehensive Cardiac Arrhythmia Sequencing Panel
Comprehensive Miscarriage, Stillbirth, and Neonatal Death Panel
Dilated Cardiomyopathy Sequencing Panel
Familial Atrial Fibrillation Syndrome Sequencing Panel
Long QT Syndrome and Jervell and Lange-Nielsen Syndrome via the KCNE1 Gene
Long QT Syndrome and Jervell and Lange-Nielsen syndrome via the KCNQ1 Gene
Long QT Syndrome via the ANK2 Gene
Long QT Syndrome via the KCNE2 Gene
Long QT Syndrome via the KCNH2 Gene
Long QT Syndrome via the SCN4B Gene
Long QT syndrome via the SNTA1 Gene
Long QT Syndrome via the AKAP9 Gene
Long QT Syndrome via the CALM2 Gene
Long QT Syndrome via the KCNJ5 Gene
Miscarriage, Stillbirth, and Neonatal Death Sequencing Panel
Primary Periodic Paralysis Sequencing Panel
Short QT Syndrome Sequencing Panel
Timothy Syndrome and Brugada Syndrome via the CACNA1C Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Ackerman MJ. et al. 2011. Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology. 13: 1077-109. PubMed ID: 21810866
  • Alders M, Mannens MMAM. Romano-Ward Syndrome. 2015. In: Pagon RA, Adam MP, Bird TD, et al., editors. GeneReviews™ [Internet]. Seattle (WA): University of Washington, Seattle. PubMed ID: 20301308
  • Cerrone M. et al. 2012. Circulation. Cardiovascular genetics. 5: 581-90. PubMed ID: 23074337
  • Human Gene Mutation Database (Bio-base).
  • Priori SG. et al. 2004. JAMA. 292: 1341-4. PubMed ID: 15367556
  • Schwartz PJ. et al. 2001. Circulation. 103: 89-95. PubMed ID: 11136691
  • Schwartz PJ. et al. 2009. Circulation. 120: 1761-7. PubMed ID: 19841298
  • Splawski I. et al. 2000. Circulation. 102: 1178-85. PubMed ID: 10973849
  • Taggart NW. et al. 2007. Circulation. 115: 2613-20. PubMed ID: 17502575
Order Kits
TEST METHODS

NextGen Sequencing

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • The first four pages of the requisition form must accompany all specimens.
  • Billing information is on the third and fourth pages.
  • Specimen and shipping instructions are listed on the fifth and sixth pages.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3-5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10-20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is good for up to 48 hours.
  • If refrigerated, blood specimen is good for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • NextGen Sequencing Tests: Send in screw cap tube at least 10 µg of purified DNA at a concentration of at least 50 µg/ml
  • Sanger Sequencing Tests: Send in a screw cap tube at least 15 µg of purified DNA at a concentration of at least 20 µg/ml. For tests involving the sequencing of more than three genes, send an additional 5 µg DNA per gene. DNA may be shipped at room temperature.
  • Deletion/Duplication via aCGH: Send in screw cap tube at least 1 µg of purified DNA at a concentration of at least 100 µg/ml.
  • Whole-Genome Chromosomal Microarray: Collect at least 5 µg of DNA in TE (10 mM Tris-cl pH 8.0, 1mM EDTA), dissolved in 200 µl at a concentration of at least 100 ng/ul (indicate concentration on tube label). DNA extracted using a column-based method (Qiagen) or bead-based technology is preferred.

CELL CULTURE

(Delivery accepted Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Ship at least two T25 flasks of confluent cells.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We do not culture cells.