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Comprehensive Cardiac Arrhythmia Sequencing Panel

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

Sequencing

Test Code TestCPT Code Copy CPT Codes
2607 ABCC9 81479 Add to Order
AKAP9 81479
ANK2 81479
CACNA1C 81479
CACNA2D1 81479
CACNB2 81406
CALM1 81479
CALM2 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 81280
KCNE3 81479
KCNE5 81479
KCNH2 81406
KCNJ2 81403
KCNJ5 81479
KCNJ8 81479
KCNQ1 81406
NKX2-5 81479
NPPA 81479
PKP2 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
TRDN 81479
TRPM4 81479
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 to Order
Pricing Comment

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 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).

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Deletion/Duplication Testing via aCGH

Test Code TestIndividual 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 81282
KCNE3$690.00 81479
KCNH2$690.00 81479
KCNJ2$690.00 81479
KCNJ5$690.00 81479
KCNQ1$690.00 81479
NKX2-5$690.00 81479
PKP2$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
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 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 CACNA2D1, CACNB2, CAV3, DES, DSP, GJA5, GPD1L, KCNA5, KCNH2, KCNJ2, KCNQ1, NKX2-5, PKP2, RYR2 and SCN5A as individual cases (Human Gene Mutation Database).

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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) 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

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. 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 (CACNA2D1CACNB2CAVDESDSPGJA5,GPD1LKCNA5KCNH2KCNJ2KCNQ1NKX2-5PKP2RYR2 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


*Limited cases

Testing Strategy

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.

Diseases

Name Inheritance OMIM ID
Andersen Tawil Syndrome 170390
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 1 107970
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 10 610193
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 11 610476
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 12 611528
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 2 600996
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 5 604400
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 8 607450
Arrhythmogenic Right Ventricular Cardiomyopathy, Type 9 609040
Atrial Fibrillation, Familial, 10 614022
Atrial Fibrillation, Familial, 11 614049
Atrial Fibrillation, Familial, 12 614050
Atrial Fibrillation, Familial, 14 615378
Atrial Fibrillation, Familial, 3 607554
Atrial Fibrillation, Familial, 4 611493
Atrial Fibrillation, Familial, 6 612201
Atrial Fibrillation, Familial, 7 612240
Atrial Fibrillation, Familial, 9 613980
Brugada Syndrome 1 601144
Brugada Syndrome 2 611777
Brugada Syndrome 3 611875
Brugada Syndrome 4 611876
Brugada Syndrome 5 612838
Brugada Syndrome 6 613119
Brugada Syndrome 7 613120
Brugada Syndrome 8 613123
Brugada Syndrome 9 616399
Catecholaminergic Polymorphic Ventricular Tachycardia, 1 604772
Catecholaminergic Polymorphic Ventricular Tachycardia, 4 614916
Catecholaminergic Polymorphic Ventricular Tachycardia, 5, with or without Muscle Weakness 615441
Familial Hypertrophic Cardiomyopathy 1 192600
Long QT Syndrome 1 192500
Long QT Syndrome 10 611819
Long QT Syndrome 11 611820
Long QT Syndrome 12 612955
Long QT Syndrome 13 613485
Long QT Syndrome 14 616247
Long QT Syndrome 15 616249
Long QT Syndrome 2 613688
Long QT Syndrome 3 603830
Long QT Syndrome 4 600919
Long QT Syndrome 5 613695
Long QT Syndrome 6 613693
Long QT Syndrome 9 611818
Short QT Syndrome 1 609620
Short QT Syndrome 2 609621
Short QT Syndrome 3 609622
Sick Sinus Syndrome 2, Autosomal Dominant 163800
Timothy Syndrome 601005
Ventricular Tachycardia, Catecholaminergic Polymorphic, 2 611938

Related Tests

Name
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 NPPA Gene
Atrial Fibrillation via the GJA5 Gene
Atrial Fibrillation via the SCN2B Gene
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 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 Miscarriage, Stillbirth, and Neonatal Death Panel
Comprehensive Neuromuscular Sequencing Panel
Congenital Hypothyroidism and Thyroid Hormone Resistance Sequencing Panel
Dilated Cardiomyopathy Sequencing Panel
Distal Hereditary Myopathy Sequencing Panel
Early Infantile Epileptic Encephalopathy Sequencing Panel
Early Infantile Epileptic Encephalopathy:
Dominant and X-linked Sequencing Panel
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
Generalized Epilepsy with Febrile Seizures Plus and Dravet syndrome via the SCN1B Gene
Heterotaxy, Situs Inversus and Kartagener's Syndrome Sequencing Panel
Isolated Nonsyndromic Congenital Heart Defects via the NKX2-5 Gene
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
Miscarriage, Stillbirth, and Neonatal Death Sequencing Panel
Myofibrillar Myopathy Sequencing Panel
Myofibrillar Myopathy via the DES Gene
Naxos Disease and Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia via the JUP Gene
Primary Aldosteronism Sequencing Panel
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
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
  • 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
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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.