Forms

Comprehensive Cardiac Arrhythmia Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
2607 ABCC9 81479 Add to Order
AKAP9 81479
ANK2 81479
CACNA1C 81479
CACNA2D1 81479
CACNB2 81406
CALM1 81479
CALM2 81479
CALM3 81479
CASQ2 81405
CAV3 81404
DES 81405
DSC2 81406
DSG2 81406
DSP 81406
GJA5 81479
GPD1L 81479
HCN4 81479
JUP 81406
KCNA5 81479
KCND3 81479
KCNE1 81479
KCNE2 81479
KCNE3 81479
KCNE5 81479
KCNH2 81406
KCNJ2 81403
KCNJ5 81479
KCNJ8 81479
KCNK3 81479
KCNQ1 81406
LDB3 81406
MYH6 81407
MYL4 81479
NKX2-5 81479
NPPA 81479
PKP2 81406
PLN 81403
PRKAG2 81406
RANGRF 81479
RYR2 81408
SCN10A 81479
SCN1B 81404
SCN2B 81479
SCN3B 81479
SCN4B 81479
SCN5A 81407
SLMAP 81479
SNTA1 81479
TGFB3 81479
TMEM43 81406
TNNI3 81405
TNNI3K 81479
TRDN 81479
TRPM4 81479
Full Panel Price* $2390.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
2607 Genes x (55) $2390.00 81403(x2), 81404(x2), 81405(x3), 81406(x11), 81407(x2), 81408, 81479(x34) Add to Order
Pricing Comment

CPT code 81413 can be used if at least 10 genes (including ANK2, CASQ2, CAV3, KCNE1, KCNE2, KCNH2, KCNJ2, KCNQ1, RYR1, and SCN5A) are sequenced. If you would like to order a subset of these genes contact us to discuss pricing.

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 use of this NGS panel will allow detection of a pathogenic variant in: ~73% of patients with autosomal dominant or sporadic Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia (McNally et al. 2014; Bhuiyan et al. 2009), ~52%-60% of Catecholaminergic Polymorphic Ventricular Tachycardia cases (Napolitano et al. 2014), ~ 80% of patients with Long QT syndrome (Splawski et al. 2000; Taggart et al 2007; Ackerman et al. 2011); 20%-35% of Brugada syndrome cases (Kapplinger et al 2010; Crotti et al. 2012); and 15%-20% of Short QT Syndrome cases (Schimpf et al. 2008).

See More

See Less

Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 ABCC9$690.00 81479 Add to Order
AKAP9$690.00 81479
ANK2$690.00 81479
CACNA1C$690.00 81479
CACNB2$690.00 81479
CASQ2$690.00 81479
CAV3$690.00 81479
DES$690.00 81479
DSC2$690.00 81479
DSG2$690.00 81479
DSP$690.00 81479
GJA5$690.00 81479
GPD1L$690.00 81479
HCN4$690.00 81479
JUP$690.00 81479
KCNE1$690.00 81479
KCNE2$690.00 81479
KCNE3$690.00 81479
KCNH2$690.00 81479
KCNJ2$690.00 81479
KCNJ5$690.00 81479
KCNQ1$690.00 81479
LDB3$690.00 81479
MYH6$690.00 81479
NKX2-5$690.00 81479
PKP2$690.00 81479
PLN$690.00 81479
PRKAG2$690.00 81479
RYR2$690.00 81479
SCN1B$690.00 81479
SCN3B$690.00 81479
SCN4B$690.00 81479
SCN5A$690.00 81479
SNTA1$690.00 81479
TGFB3$690.00 81479
TMEM43$690.00 81479
TNNI3$690.00 81479
Full Panel Price* $1670.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (37) $1670.00 81479(x37) Add to Order
Pricing Comment

CPT code 81414 can be used if at least KCHN2 and KCNQ1 are analyzed.

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 CACNA2D1, CACNB2, CAV3, DES, DSP, GJA5, GPD1L, KCNA5, KCNH2, KCNJ2, KCNQ1, NKX2-5, PKP2, RYR2 and SCN5A as individual cases (Human Gene Mutation Database).

See More

See Less

Clinical Features

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) primarily affects 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 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 (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 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 are asymptomatic.

Short QT Syndrome (SQTS) is an inherited arrhythmia disorder which affects the movement of ions through channels within the cell membrane and is associated with marked shortening of QT intervals and sudden cardiac death in individuals with structurally normal hearts. Typical electrocardiogram (ECG) findings associated with SQTS include an abnormally short QT interval (usually <360 msec with a range of 220 to 360 msec), absence of the ST segment, and tall and peaked T waves in the precordial leads. The clinical presentation of SQTS is variable, and many patients are asymptomatic. Most patients present with one or more of the following symptoms: SCD, palpitations, syncope, and atrial fibrillation (Patel et al. 2010).

Genetics

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. 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 AKAP9 AD 7q21.2
ANK2 AD 4q25-q26 CACNA1C AD 12p13.33
CACNA2D1 AD* 7q21.11 CACNB2 AD 10p12.33-p12.31
CALM1 AD 14q32.11 CALM2 AD 2p21
CALM3 AD* 19q13.32 CASQ2 AR 1p13.1
CAV3 AD/AR 3p25.3 DES1 AD/AR 2q35
DSC2 AD/AR 18q12.1 DSG2 AD 18q12.1
DSP AD/AR 6p24.3 GJA5 AD 1q21.2
GPD1L AD 3p22.3 HCN4 AD 15q24.1
JUP AD/AR 17q21.2 KCNA5 AD 12p13.32
KCND3 AD 1p13.2 KCNE1 AD 21q22.11-q22.12
KCNE5(KCNE1L) X-linked Xq23 KCNE2 AD 21q22.11
KCNE3 AD 11q13.4 KCNH2 AD 7q36.1
KCNJ2 AD 17q24.3 KCNJ5 AD 11q24.3
KCNJ8 AD* 12p12.1 KCNK3 AD 2p23.3
KCNQ1 AD/AR 11p15.5-p15.4 LDB3 AD 10q23.2
MYH6 AD 14q11.2 MYL4 AD 17q21.32
NKX2-5 AD/AR 5q35.1 NPPA AD 1p36.22
PKP2 AD 12p11.2 PLN AD 6q22.31
PRKAG2 AD 7q36.1 RANGRF AD* 17p13.1
RYR2 AD 1q43 SCN10A AD 3p22.2
SCN1B AD 19q13.12 SCN2B AD 11q23.3
SCN3B AD 11q24.1 SCN4B AD 11q23.3
SCN5A AD 3p22.2 SLMAP AD* 3p14.3
SNTA1 AD 20q11.21 TGFB3 AD 14q24.3
TNNI3 AD/AR 19q13.42 TNNI3K AD 1p31.1
TMEM43 AD 3p25.1 TRDN AR 6q22.31
TRPM4 AD 19q13.33

*Limited cases

Testing Strategy

For this NextGen panel, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for each of the genes listed. 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.

This panel provides 100% coverage of the aforementioned regions of the indicated genes. We define 100% coverage as > 20X NGS reads for exons and 0-10 bases of flanking DNA, > 10X NGS reads for 11-20 bases of flanking DNA, or Sanger sequencing.

Indications for Test

Patients with a strong clinical suspicion for inherited cardiac arrhythmia disorder, or unexplained sudden cardiac arrest/death.

Diseases

Name Inheritance OMIM ID
Andersen Tawil Syndrome AD 170390
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 1 AD 107970
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 10 AD 610193
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 11 AD,AR 610476
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 12 AD 611528
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 2 AD 600996
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 5 AD 604400
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 8 AD 607450
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 9 AD 609040
Atrial Fibrillation, Familial, 10 AD 614022
Atrial Fibrillation, Familial, 11 AD 614049
Atrial Fibrillation, Familial, 12 AD 614050
Atrial Fibrillation, Familial, 14 AD 615378
Atrial Fibrillation, Familial, 18 AD 617280
Atrial Fibrillation, Familial, 3 AD 607554
Atrial Fibrillation, Familial, 4 AD 611493
Atrial Fibrillation, Familial, 6 AD 612201
Atrial Fibrillation, Familial, 7 AD 612240
Atrial Fibrillation, Familial, 9 AD 613980
Atrial Septal Defect 3 AD 614089
Brugada Syndrome 1 AD 601144
Brugada Syndrome 2 AD 611777
Brugada Syndrome 3 AD 611875
Brugada Syndrome 4 AD 611876
Brugada Syndrome 5 AD 612838
Brugada Syndrome 6 AD 613119
Brugada Syndrome 7 AD 613120
Brugada Syndrome 8 AD 613123
Brugada Syndrome 9 AD 616399
Cardiac Conduction Disease with or without Dilated Cardiomyopathy AR 616117
Cardiomyopathy, Familial Restrictive, 1 AD 115210
Catecholaminergic Polymorphic Ventricular Tachycardia, 1 AD 604772
Catecholaminergic Polymorphic Ventricular Tachycardia, 4 AD 614916
Catecholaminergic Polymorphic Ventricular Tachycardia, 5, with or without Muscle Weakness AD 615441
Dilated Cardiomyopathy 1C AD 601493
Dilated Cardiomyopathy 1Ee AD 613252
Dilated Cardiomyopathy 1FF AD 613286
Dilated Cardiomyopathy 1P AD 609909
Dilated Cardiomyopathy 2A AD 611880
Familial Hypertrophic Cardiomyopathy 1 AD 192600
Familial Hypertrophic Cardiomyopathy 14 AD 613251
Familial Hypertrophic Cardiomyopathy 18 AD 613874
Familial Hypertrophic Cardiomyopathy 6 AD 600858
Familial Hypertrophic Cardiomyopathy 7 AD 613690
Glycogen Storage Disease Of Heart, Lethal Congenital AD 261740
Long QT Syndrome 1 AD 192500
Long QT Syndrome 10 AD 611819
Long QT Syndrome 11 AD 611820
Long QT Syndrome 12 AR 612955
Long QT Syndrome 13 AD 613485
Long QT Syndrome 14 AD 616247
Long QT Syndrome 15 AD 616249
Long QT Syndrome 2 AD 613688
Long QT Syndrome 3 AD 603830
Long QT Syndrome 4 AD 600919
Long QT Syndrome 5 AD 613695
Long QT Syndrome 6 AD 613693
Long QT Syndrome 9 AD 611818
Myofibrillar Myopathy, ZASP-Related AD 609452
Short QT Syndrome 2 AD 609621
Short QT Syndrome 3 AD 609622
Sick Sinus Syndrome 2, Autosomal Dominant AR 163800
Sick Sinus Syndrome 3, Susceptibility To AD 614090
Timothy Syndrome AD 601005
Ventricular Tachycardia, Catecholaminergic Polymorphic, 2 AD 611938
Wolff-Parkinson-White Pattern AD 194200

Related Tests

Name
PRKAG2-Related Disorders via the PRKAG2 Gene
Andersen-Tawil Syndrome/Long QT Syndrome via the KCNJ2 Gene
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia and DSP-Related Disorders via the DSP Gene
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia Sequencing Panel
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the DSC2 Gene
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the DSG2 Gene
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the PKP2 Gene
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the TGFB3 Gene
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the TMEM43 Gene
Atrial Fibrillation Syndrome via the KCNA5 Gene
Atrial Fibrillation Syndrome via the KCNE5 Gene
Atrial Fibrillation Syndrome via the MYL4 Gene
Atrial Fibrillation Syndrome via the NPPA Gene
Atrial Fibrillation via the GJA5 Gene
Atrial Fibrillation via the SCN2B Gene
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Autosomal Dominant Limb Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Autosomal Recessive Limb Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Brugada Syndrome 1 via the SCN5A Gene
Brugada Syndrome Sequencing Panel
Brugada Syndrome via the CACNA2D1 Gene
Brugada Syndrome via the CACNB2 Gene
Brugada Syndrome via the GPD1L Gene
Brugada Syndrome via the RANGRF Gene
Brugada Syndrome via the SCN1B Gene
Brugada Syndrome via the SCN3B Gene
Brugada Syndrome via the SLMAP Gene
Brugada Syndrome via the KCND3 Gene
Brugada Syndrome via the KCNE3 Gene
Cantu Syndrome via the ABCC9 Gene
Catecholaminergic Polymorphic Ventricular Tachycardia and Long QT Syndrome via the CALM1 Gene
Catecholaminergic Polymorphic Ventricular Tachycardia Sequencing Panel
Catecholaminergic Polymorphic Ventricular Tachycardia via the CASQ2 Gene
Catecholaminergic Polymorphic Ventricular Tachycardia via the RYR2 Gene
Catecholaminergic Polymorphic Ventricular Tachycardia via the TRDN Gene
Caveolinopathy via the CAV3 Gene
Ciliopathy Sequencing Panel
Comprehensive Cardiology Sequencing Panel with CNV Detection
Comprehensive Neuromuscular Sequencing Panel
Congenital Hypothyroidism and Thyroid Hormone Resistance Sequencing Panel
Dilated Cardiomyopathy Sequencing Panel with CNV Detection
Distal Hereditary Myopathy Sequencing Panel
Early Infantile Epileptic Encephalopathy Sequencing Panel
Early Infantile Epileptic Encephalopathy:
Dominant and X-linked Sequencing Panel
Epidermolysis Bullosa and Related Disorders Sequencing Panel with CNV Detection
Epilepsy: Dravet Syndrome Sequencing Panel
Epilepsy: Generalized Epilepsy with Febrile Seizures Plus (GEFS+) Sequencing Panel
Episodic Pain Syndrome Sequencing Panel
Familial Atrial Fibrillation Syndrome Sequencing Panel
Familial Episodic Pain Type 2 Syndrome via the SCN10A Gene
Fetal Concerns Sequencing Panel with CNV Detection
Generalized Epilepsy with Febrile Seizures Plus and Dravet syndrome via the SCN1B Gene
Glycogen Storage Disease and Disorders of Glucose Metabolism Sequencing Panel
Heterotaxy, Situs Inversus and Kartagener's Syndrome Sequencing Panel
Hypertrophic Cardiomyopathy and Dilated Cardiomyopathy via the MYH6 Gene
Hypertrophic Cardiomyopathy and Dilated Cardiomyopathy via the PLN Gene
Hypertrophic Cardiomyopathy and other MYH7-Related Disorders via the MYH7 Gene
Hypertrophic Cardiomyopathy and Related Disorders via the TNNI3 Gene
Hypertrophic Cardiomyopathy Sequencing Panel with CNV Detection
Isolated Nonsyndromic Congenital Heart Defects via the NKX2-5 Gene
Left Ventricular Noncompaction (LVNC) Sequencing Panel with CNV Detection
Limb-Girdle Muscular Dystrophy (LGMD) 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 Sequencing Panel
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
Myofibrillar Myopathy Sequencing Panel
Myofibrillar Myopathy via the DES Gene
Myofibrillar Myopathy via the LDB3 (ZASP) Gene
Naxos Disease and Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the JUP Gene
Pan Cardiomyopathy Sequencing Panel with CNV Detection
Primary Aldosteronism Sequencing Panel with CNV Detection
Primary Periodic Paralysis Sequencing Panel
Progressive Familial Heart Block via the TRPM4 Gene
Short QT Syndrome Sequencing Panel
Sick Sinus Syndrome and Brugada Syndrome via the HCN4 Gene
Sudden Cardiac Arrest Sequencing Panel with CNV Detection
Timothy Syndrome and Brugada Syndrome via the CACNA1C Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Ackerman M.J. et al. 2011. Europace. 13: 1077-109. PubMed ID: 21810866
  • Bhuiyan Z.A. 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 J.D. et al. 2010. Heart Rhythm. 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 P.J. et al. 2001. Circulation. 103: 89-95. PubMed ID: 11136691
  • Splawski I. et al. 2000. Circulation. 102: 1178-85. PubMed ID: 10973849
  • Taggart N.W. et al. 2007. Circulation. 115: 2613-20. PubMed ID: 17502575
Order Kits
TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

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
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -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 ml -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 stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
loading Loading... ×