Comprehensive Cardiac Arrhythmia Sequencing Panel
- Summary and Pricing
- Clinical Features and Genetics
|Test Code||Test||CPT Code Copy CPT Codes|
|Full Panel Price*||$2390.00|
|Test Code||Test||Total Price||CPT Codes Copy CPT Codes|
|2607||Genes x (46)||$2390.00||81280, 81403, 81404(x2), 81405(x2), 81406(x9), 81407, 81408, 81479(x29)||Add|
If you would like to order a subset of these genes contact us to discuss pricing.
For ordering targeted known variants, please proceed to our Targeted Variants landing page.
The great majority of tests are completed within 28 days.
It is estimated that this NGS panel can detect a pathogenic variant in: ~73% of patients with autosomal dominant or sporadic ARVC/D (McNally et al. 2009; Bhuiyan et al. 2009), ~52%-60% of CPVT cases (Napolitano et al. 2014), ~ 80% of patients with LQTS (Splawski et al. 2000; Taggart et al 2007; Ackerman et al. 2011); 20%-35% of BrS cases (Kapplinger et al 2010; Crotti et al. 2012); and 15%-20% of SQTS cases (Schimpf et al. 2008).
Deletion/Duplication Testing via aCGH
|Test Code||Test||Individual Gene Price||CPT Code Copy CPT Codes|
|Full Panel Price*||$1670.00|
|Test Code||Test||Total Price||CPT Codes Copy CPT Codes|
|600||Genes x (32)||$1670.00||81282, 81479(x31)||Add|
# of Genes Ordered
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The great majority of tests are completed within 28 days.
Gross deletions or duplications not detectable by Sanger sequencing have been reported in CACNA2D1, CACNB2, CAV3, DES, DSP, GJA5, GPD1L, KCNA5, KCNH2, KCNJ2, KCNQ1, NKX2-5, PKP2, RYR2 and SCN5A as individual cases (Human Gene Mutation Database).
Cardiac arrhythmia is a group of conditions in which the heartbeat is irregular, too fast, or too slow. Some arrhythmia disorders are inherited, including Arrhythmogenic Right Ventricular Dysplasia/ Cardiomyopathy (ARVD/C), Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT), Brugada syndrome, long QT syndrome, and Short QT syndrome.
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia (ARVC/D) is a heart disease primarily affecting the right ventricle. It is characterized by myocardial atrophy, fibrofatty replacement of the ventricular myocardium and inflammatory infiltrates (McNally et al. 2014). With disease progression and occasional left ventricle involvement, heart failure may result. ARVC/D is present in ~20% of young sudden cardiac death victims (Corrado et al. 1998). ARVC/D affects between 1/1000 and 1/5000 people worldwide with a higher prevalence in men compared to women (Corrado and Thiene 2006).
Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) is an inherited arrhythmogenic heart disorder characterized by life-threatening electrical instability induced by physical or emotional stress without any structural cardiac abnormalities (Napolitano et al. 2014). The electrical instability may degenerate into cardiac arrest and sudden death. CPVT typically onsets during childhood and often presents as syncope.
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).
Brugada syndrome (BrS) is a potentially life-threating cardiac arrhythmia disorder without structural abnormalities, characterized by dizziness, syncope, nocturnal agonal respiration and sudden death. The classic electrocardiographic findings associated with BrS include ST segment elevation in leads V1 to V3, right bundle branch block, first degree AV block, and intraventricular conduction delay. BrS is much more common in men than in women, and many people who have BrS don't have symptoms.
Short QT Syndrome (SQTS) is an inherited arrhythmia disorder (which affects the movement of ions through channels within the cell membrane) associated with marked shortening of QT intervals and sudden cardiac death (SCD) in individuals with structurally normal hearts. Typical electrocardiogram (ECG) findings associated with SQTS include an abnormally short QT interval (usually
Cardiac arrhythmia disorder is a heterogeneous disease usually inherited in an autosomal dominant (AD), but occasionally in an autosomal recessive (AR) manner with age- and gender-dependent penetrance. Most of the genes involved encode subunits of ion channels (sodium, potassium calcium channels) or the proteins that regulate them in cardiac contraction unit or conduction system. This panel includes 46 genes. A wide variety of causative variants (missense, nonsense, splicing, small deletions and insertions) have been reported. Large deletions/duplications and complex genomic rearrangements have also been reported in a few genes (CACNA2D1, CACNB2, CAV, DES, DSP, GJA5,GPD1L, KCNA5, KCNH2, KCNJ2, KCNQ1, NKX2-5, PKP2, RYR2 and SCN5A) (Human Gene Mutation Database). See individual gene test descriptions for more information on molecular biology of gene products.
The following Table indicates chromosome location and mode of inheritance by gene.
GENE INHERITANCE CHR LOCATION GENE INHERITANCE CHR LOCATION
ABCC9 AD 12p12.1 KCNE3 AD 11q13.4
AKAP9 AD 7q21.2 KCNH2 AD 7q36.1
ANK2 AD 4q25-q26 KCNJ2 AD 17q24.3
CACNA1C AD 12p13.33 KCNJ5 AD 11q24.3
CACNA2D1 AD* 7q21.11 KCNJ8 AD* 12p12.1
CACNB2 AD 10p12.33-p12.31 KCNQ1 AD/AR 11p15.5-p15.4
CALM1 AD 14q32.11 NKX2-5 AD/AR 5q35.1
CALM2 AD 2p21 NPPA AD 1p36.22
CASQ2 AR 1p13.1 PKP2 AD 12p11.21
CAV3 AD/AR 3p25.3 RANGRF AD* 17p13.1
DES AD/AR 2q35 RYR2 AD 1q43
DSC2 AD/AR 18q12.1 SCN10A AD 3p22.2
DSG2 AD 18q12.1 SCN1B AD 19q13.12
DSP AD/AR 6p24.3 SCN2B AD 11q23.3
GJA5 AD 1q21.2 SCN3B AD 11q24.1
GPD1L AD 3p22.3 SCN4B AD 11q23.3
HCN4 AD 15q24.1 SCN5A AD 3p22.2
JUP AD/AR 17q21.2 SLMAP AD* 3p14.3
KCNA5 AD 12p13.32 SNTA1 AD 20q11.21
KCND3 AD 1p13.2 TGFB3 AD 14q24.3
KCNE1 AD 21q22.11-q22.12 TMEM43 AD 3p25.1
KCNE5 (KCNE1L) X-linked Xq23 TRDN AR 6q22.31
KCNE2 AD 21q22.11 TRPM4 AD 19q13.33
For this Next Generation (NextGen) panel, we sequence all coding exons of the genes listed below, plus ~20 nucleotides of flanking DNA for each exon. 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 and undocumented variants are confirmed by Sanger sequencing.
Indications for Test
Patients with a strong clinical suspicion for inherited cardiac arrhythmia disorder, or unexplained sudden cardiac arrest/death.
- Genetic Counselor Team - email@example.com
- Guoli Sun, MD, PhD, FACMG - firstname.lastname@example.org
- 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
- Bhuiyan ZA et al. 2009. Circulation. Cardiovascular Genetics. 2: 418-27. PubMed ID: 20031616
- Cerrone M. et al. 2012. Circulation. Cardiovascular genetics. 5: 581-90. PubMed ID: 23074337
- Corrado D. et al. 1998. The New England Journal of Medicine. 339: 364-9. PubMed ID: 9691102
- Corrado D., Thiene G. 2006. Circulation. 113: 1634-7. PubMed ID: 16585401
- Crotti L. et al. 2012. Journal of the American College of Cardiology. 60: 1410-8. PubMed ID: 22840528
- Human Gene Mutation Database (Bio-base).
- Kapplinger JD. et al. 2010. Heart rhythm : the official journal of the Heart Rhythm Society. 7: 33-46. PubMed ID: 20129283
- McNally E. et al. 2014. Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy, Autosomal Dominant. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301310
- Napolitano, C. et al. 2014. Catecholaminergic Polymorphic Ventricular Tachycardia. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301466
- Patel C. et al. 2010. Circulation. Arrhythmia and Electrophysiology. 3: 401-8. PubMed ID: 20716721
- Schimpf R. et al. 2008. Current Opinion in Cardiology. 23:192-8. PubMed ID: 18382206
- Schwartz PJ. et al. 2001. Circulation. 103: 89-95. PubMed ID: 11136691
- Splawski I. et al. 2000. Circulation. 102: 1178-85. PubMed ID: 10973849
- Taggart NW. et al. 2007. Circulation. 115: 2613-20. PubMed ID: 17502575
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.
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.
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
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.
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.
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.
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.
- 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.
(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.
(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.
(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.