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Comprehensive Neuropathy Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
3441 AARS 81479 Add to Order
AIFM1 81479
ATL1 81406
ATP7A 81479
BICD2 81479
BSCL2 81406
CCT5 81479
COX6A1 81479
DCTN1 81479
DHTKD1 81479
DNAJB2 81479
DNM2 81479
DNMT1 81479
DYNC1H1 81479
EGR2 81404
FAM134B 81479
FBLN5 81479
FGD4 81479
FIG4 81406
GAN 81479
GARS 81406
GDAP1 81405
GJB1 81403
GNB4 81479
HINT1 81479
HK1 81479
HSPB1 81404
HSPB3 81479
HSPB8 81479
IGHMBP2 81479
IKBKAP 81479
INF2 81406
KARS 81479
KIF1A 81479
KIF5A 81479
LAS1L 81479
LITAF 81404
LMNA 81406
LRSAM1 81479
MARS 81479
MED25 81479
MEGF10 81479
MFN2 81406
MPZ 81405
MTMR2 81479
NDRG1 81479
NEFL 81405
NGF 81479
NTRK1 81479
PDK3 81479
PLEKHG5 81479
PMP22 81325
PRPS1 81479
PRX 81405
RAB7A 81405
REEP1 81405
SBF1 81479
SBF2 81479
SCN9A 81479
SETX 81406
SH3TC2 81406
SLC12A6 81479
SLC5A7 81479
SPTLC1 81479
SPTLC2 81479
TFG 81479
TRIM2 81479
TRPV4 81479
TTR 81404
WNK1 81479
YARS 81479
Full Panel Price* $1990.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
3441 Genes x (71) $1990.00 81325, 81403, 81404(x4), 81405(x6), 81406(x9), 81479(x50) 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

A genetic etiology can be identified in approximately 50-70% of individuals with CMT (Saporta et al. 2011; Rossor et al. 2013). Specifically, a molecular diagnosis can be identified in approximately 80-85% of individuals with demyelinating neuropathy (CMT1), and a molecular diagnosis can be identified in approximately 25-35% of individuals with axonal neuropathy (CMT2) (Bird 2015; Bird 2015; Rossor et al. 2013). Only about 20% of patients with distal hereditary motor neuropathy or hereditary sensory and autonomic neuropathy will obtain a genetic diagnosis (Rossor et al. 2012; Rotthier et al. 2009). The sensitivity of this panel will vary based on the clinical phenotype of the patient.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 AARS$690.00 81479 Add to Order
AIFM1$690.00 81479
ATP7A$690.00 81479
BSCL2$690.00 81479
COX6A1$690.00 81479
DCTN1$690.00 81479
DHTKD1$690.00 81479
DNM2$690.00 81479
DNMT1$690.00 81479
EGR2$690.00 81479
FBLN5$690.00 81479
FGD4$690.00 81479
FIG4$690.00 81479
GAN$690.00 81479
GARS$690.00 81479
GDAP1$690.00 81479
GJB1$690.00 81479
GNB4$690.00 81479
HINT1$690.00 81479
HK1$690.00 81479
HSPB1$690.00 81479
HSPB8$690.00 81479
IGHMBP2$690.00 81479
INF2$690.00 81479
KARS$690.00 81479
KIF5A$690.00 81479
LAS1L$690.00 81479
LITAF$690.00 81479
LMNA$690.00 81479
LRSAM1$690.00 81479
MARS$690.00 81479
MED25$690.00 81479
MEGF10$690.00 81479
MFN2$690.00 81479
MPZ$690.00 81479
MTMR2$690.00 81479
NDRG1$690.00 81479
NEFL$690.00 81479
PDK3$690.00 81479
PLEKHG5$690.00 81479
PMP22$690.00 81324
PRPS1$690.00 81479
PRX$690.00 81479
RAB7A$690.00 81479
REEP1$690.00 81479
SBF1$690.00 81479
SBF2$690.00 81479
SCN9A$690.00 81479
SETX$690.00 81479
SH3TC2$690.00 81479
SLC5A7$690.00 81479
TRIM2$690.00 81479
TRPV4$690.00 81479
TTR$690.00 81479
WNK1$690.00 81479
YARS$690.00 81479
Full Panel Price* $1670.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (56) $1670.00 81324, 81479(x55) 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

It is estimated that ~70% of all Charcot Marie Tooth Type 1 (CMT1) is due to the PMP22 1.5 Mb duplication, while only around 5% of CMT1 cases are due to point mutations (Bird 2015). The NGS sequencing panel will not detect the common 1.5 Mb duplication or deletion in the PMP22 gene; however, PMP22 deletion/duplication testing via aCGH can be ordered through test code #600. Although the 1.5 Mb duplication/deletion are the most common copy number variants in PMP22, many other deletions/duplications within this region have been reported and will also be detected by aCGH analysis (Zhang et al. 2010). Clinical sensitivity of other genes in this panel is expected to be low because relatively few gross deletions/insertions/duplications have been reported (Human Gene Mutation Database).

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Clinical Features

This comprehensive panel includes genes that are causative for Charcot-Marie-Tooth disease (CMT), hereditary motor neuropathies and hereditary sensory and autonomic neuropathies (HSAN). These inherited neuropathies of the peripheral nervous system are genetically and phenotypically heterogeneous.

Charcot Marie Tooth disease (CMT), also known as hereditary motor and sensory neuropathy (HMSN) is a large group of inherited disorders of the peripheral nerves. The progressive degeneration of motor nerves results in weakness and atrophy of the distal muscles. The degeneration of sensory nerves leads to decreased sensation, tingling and numbness in the legs, feet, arms and hands and neuropathic pain. The age of onset varies from childhood to mid adulthood. Symptoms usually begin with weakness and atrophy in the muscles of the legs and feet. As the disease progresses, weakness and atrophy of the muscles of the arms and hands may occur. CMT is heterogeneous in regards to symptoms, severity and progression rate. Although the disease may lead to disability and respiratory difficulty, life expectancy is usually unaffected. Most common symptoms include foot deformity, loss of balance, hammertoes, foot drop, frequent tripping and falls, and reduced manual dexterity (Bird 2015). Diagnosis is based on clinical features, family history, neurological examination, and electromyography (EMG) and nerve conduction velocity (NCV) findings (Rossor 2013; Bird 2015). CMT affects approximately 1 in 3,300 people (Bird 2015; Saporta 2011). Demyelinating forms of CMT primarily affect the myelin sheath of the peripheral nerve and are characterized by slow nerve conduction velocities (NCV) of less than 38 m/s in upper limbs. Axonal forms of CMT primarily affect the axons of the peripheral nerves and are characterized by normal or almost normal NCV of greater than 38 m/s. Intermediate NCV of 25-45 m/s can be difficult to classify as axonal or demyelinating. Approximately 70% of CMT1 is caused by the recurrent 1.5 Mb duplication of chromosome 17p11.2 which includes the PMP22 gene (Bird 2015; Li et al. 2013; van Paassen et al. 2014).

Hereditary sensory and autonomic neuropathy (HSAN) is a heterogeneous group of slowly-progressing neurological diseases characterized by progressive dysfunction of peripheral sensory nerves (Auer-Grumbach 2013). Many patients with HSAN manifest loss of pain and temperature sensation which can lead to chronic skin ulcers, and even osteomyelitis and necrosis (Auer-Grumbach et al. 2003, 2008). HSAN affects approximately 1 in 25,000 people (Axelrod and Gold-von Simson 2007, Auer-Grumbach 2008, 2013, Davidson et al. 2012).

Distal hereditary motor neuropathy (dHMN) is a clinically and genetically heterogeneous group of disorders characterized by progressive distal motor weakness and atrophy. The distribution of weakness is usually greater in the distal lower limbs than the upper limbs, and weakness of the toe extensor muscles is often the presenting sign. Nerve conduction velocities are generally normal in dHMN, and sensory impairment is not a feature of this disorder. Subtypes of dHMN can be differentiated to some extent based on age of onset, pattern of weakness, rate of progression, and appearance of additional complicating features. For discussions on classification, pathophysiology, and molecular genetics of dHMN see Irobi et al. (2004) and Drew et al. (2011).

Genetics

Charcot-Marie-Tooth can be inherited in an autosomal dominant, autosomal recessive or an X-linked manner. The MPZ, LITAF, NEFL, PMP22, FBLN5, MFN2, YARS, RAB7, TRPV4, GARS, HSPB1, HSPB8, INF2, GNB4, AARS, DYNC1H1, LRSAM1, DHTKD1, MARS, KIF5A genes are involved in autosomal dominant CMT. Autosomal recessive forms of CMT involve the LMNA, MED25, HINT1, TRIM2, MTMR2, SBF2, SBF1, SH3TC2, PRX, FGD4, FIG4, NDRG1, HK1, KARS, CTDP1, PLEKHG5, IGHMBP2 and COX6A1 genes. Pathogenic variants in the EGR2, GDAP1, and DNM2 genes can exhibit both dominant and recessive inheritance. In cases of Dejerine-Sottas syndrome, the PMP22, MPZ, EGR2, and PRX genes can exhibit both dominant and recessive inheritance as well. Pathogenic variants in the GJB1, AIFM1, PRPS1, and PDK3 genes are inherited in an X-linked manner. See individual gene test descriptions for information on molecular biology of gene products.

HSAN 1 is inherited in an autosomal dominant (AD) manner and can be caused by pathogenic variants in multiple genes including SPTLC1 and SPTLC2 (serine palmitoyltransferase), ATL1 (atlastin-1), and DNMT1 (DNA methyltransferase 1). HSAN 2-5 typically exhibit an autosomal recessive (AR) form of inheritance (Axelrod and Gold-von Simson. 2007). HSAN 2 is associated with WNK1 (WNK lysine deficient protein kinase 1), FAM13B (family with sequence similarity 13B), KIF1A(kinesin family member 1A), and SCN9A (sodium voltage-gated channel alpha subunit 9). HSAN 3-5 are caused by pathogenic variants in IKBKAP (IkappaB Kinase Complex-Associated Protein), NTRK1 (neurotrophic tyrosine kinase, receptor, type1) and NGFB (nerve growth factor beta), respectively (Axelrod and Gold-von Simson. 2007). CCT5 pathogenic variants can cause another autosomal recessive type of HSNA which does not fit into the current five classifications.

Distal hereditary motor neuropathies can be inherited as autosomal dominant, autosomal recessive, or X-linked conditions. Genes that are involved in dominantly inherited dHMN include HSPB1, HSPB8, SETX, GARS, BSCL2, SLC5A7, DCTN1, TRPV4, and REEP1. Recessively inherited forms of dHMN are caused by pathogenic variants in the IGHMBP2, GAN,and HINT1 genes. Two X-linked forms are also known (ATP7A and LAS1L).

Testing Strategy

For this NGS test, greater than 99% of exonic 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 method, followed by massively parallel sequencing of the captured DNA fragments. All pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing. Please note that for technical reasons, exon 8 of the INF2 gene is not currently included in this panel. Thus far, only exons 2 to 6, especially exons 2 to 4 that encode the diaphanous inhibitory domain (DID), have been reported to harbor pathogenic INF2 variants (Boyer et al. 2011; Barua et al. 2013; Human Gene Mutation Database).

Indications for Test

Any patient with clinical symptoms consistent with a peripheral neuropathy.

Diseases

Name Inheritance OMIM ID
Amyloidogenic Transthyretin Amyloidosis AD 105210
Andermann Syndrome AR 218000
Charcot-Marie-Tooth Disease Dominant Intermediate 3 AD 607791
Charcot-Marie-Tooth Disease Type 2B AR 600882
Charcot-Marie-Tooth Disease Type 2B1 AR 605588
Charcot-Marie-Tooth Disease Type 2B2 AR 605589
Charcot-Marie-Tooth Disease Type 2C AR 606071
Charcot-Marie-Tooth Disease Type 2D AR 601472
Charcot-Marie-Tooth Disease Type 2E AR 607684
Charcot-Marie-Tooth Disease Type 2F AR 606595
Charcot-Marie-Tooth Disease Type 2I AR 607677
Charcot-Marie-Tooth Disease Type 2J AR 607736
Charcot-Marie-Tooth Disease Type 2K AR 607831
Charcot-Marie-Tooth Disease, Axonal, Type 2O AR 614228
Charcot-Marie-Tooth Disease, Axonal, With Vocal Cord Paresis, Autosomal Recessive AR 607706
Charcot-Marie-Tooth Disease, Dominant Intermediate B AD 606482
Charcot-Marie-Tooth Disease, Dominant Intermediate C AD 608323
Charcot-Marie-Tooth Disease, Dominant Intermediate E AD 614455
Charcot-Marie-Tooth Disease, Dominant Intermediate F AD 615185
Charcot-Marie-Tooth Disease, Recessive Intermediate A AR 608340
Charcot-Marie-Tooth Disease, Recessive Intermediate B AR 613641
Charcot-Marie-Tooth Disease, Recessive Intermediate C AR 615376
Charcot-Marie-Tooth Disease, Recessive Intermediate D AR 616039
Charcot-Marie-Tooth Disease, Type 1A AD 118220
Charcot-Marie-Tooth Disease, Type 1D AD 607678
Charcot-Marie-Tooth Disease, Type 1E AD 118300
Charcot-Marie-Tooth Disease, Type 1F AD 607734
Charcot-Marie-Tooth Disease, Type 2A2 AR 609260
Charcot-Marie-Tooth Disease, Type 2L AR 608673
Charcot-Marie-Tooth Disease, Type 2N AR 613287
Charcot-Marie-Tooth Disease, Type 2Q AD 615025
Charcot-Marie-Tooth Disease, Type 2R XL 615490
Charcot-Marie-Tooth Disease, Type 2S AR 616155
Charcot-Marie-Tooth Disease, Type 2T AR 616233
Charcot-Marie-Tooth Disease, Type 2U AD 616280
Charcot-Marie-Tooth Disease, Type 3 AR, AD 145900
Charcot-Marie-Tooth Disease, Type 4A AR 214400
Charcot-Marie-Tooth Disease, Type 4B1 AR 601382
Charcot-Marie-Tooth Disease, Type 4B2 AR 604563
Charcot-Marie-Tooth Disease, Type 4B3 AR 615284
Charcot-Marie-Tooth Disease, Type 4C AR 601596
Charcot-Marie-Tooth Disease, Type 4D AR 601455
Charcot-Marie-Tooth Disease, Type 4E AR 605253
Charcot-Marie-Tooth Disease, Type 4F AR 614895
Charcot-Marie-Tooth Disease, Type 4H AR 609311
Charcot-Marie-Tooth Disease, Type 4J AR 611228
Charcot-Marie-Tooth Disease, Type Ib AD 118200
Charcot-Marie-Tooth Disease, Type IC AD 601098
Charcot-Marie-Tooth Disease, X-Linked Dominant, 1 XLD 302800
Charcot-Marie-Tooth Disease, X-linked Dominant, 6 AR 300905
Charcot-Marie-Tooth Disease, X-Linked Recessive, Type 5 XLR 311070
Charcot-Marie-Toothe Disease, Type 2P AD,AR 614436
Cowchock Syndrome XL 310490
Distal Hereditary Motor Neuronopathy Type 2A AD 158590
Distal Hereditary Motor Neuronopathy Type 2B AD 608634
Distal Hereditary Motor Neuronopathy Type 5 AD 600794
Familial Dysautonomia AR 223900
Giant Axonal Neuropathy AD 256850
Hereditary Insensitivity To Pain With Anhidrosis AR 256800
Indifference To Pain, Congenital, Autosomal Recessive AR 243000
Myopathy, Early-Onset, Areflexia, Respiratory Distress, And Dysphagia AR 614399
Neuromyotonia and axonal neuropathy, autosomal recessive AR 137200
Neuronopathy, Distal Hereditary Motor, Type VIIB AD 607641
Neuronopathy, Distal Hereditary Motor, Type IIC AD 613376
Neuronopathy, Distal Hereditary Motor, Type VB AD 614751
Neuronopathy, Distal Hereditary Motor, Type VIIA AR 158580
Neuropathy, Hereditary Motor and Sensory, Okinawa Type AD 604484
Neuropathy, Hereditary Motor and Sensory, Russe Type AR 605285
Neuropathy, Hereditary Motor and Sensory, Type VIA AD 601152
Neuropathy, Hereditary Sensory And Autonomic, Type 1A AD 162400
Neuropathy, Hereditary Sensory And Autonomic, Type IC AR 613640
Neuropathy, Hereditary Sensory And Autonomic, Type IIA AR 201300
Neuropathy, Hereditary Sensory And Autonomic, Type IIB AR 613115
Neuropathy, Hereditary Sensory And Autonomic, Type V AR 608654
Neuropathy, Hereditary Sensory, Type ID AD 613708
Neuropathy, Hereditary Sensory, Type IE AD 614116
Neuropathy, Hereditary Sensory, Type IIC AR 614213
Neuropathy, Hereditary Sensory, With Spastic Paraplegia AR 256840
Neuropathy, Hereditary, with or without Age-Related Macular Degeneration AD 608895
Spinal Muscular Atrophy, Distal, X-Linked 3 XL 300489
Spinal Muscular Atrophy, Lower Extremity-Predominant, 2 AD 615290
Spinocerebellar Ataxia Autosomal Recessive 1 AR 606002

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Name
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LAS1L-Related Disorders via the LAS1L Gene
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MPZ-Related Neuropathies
PMP22-Related Neuropathies
PRPS1-Related Disorders
REEP1-Related Disorders via the REEP1 Gene
TFG-Related Disorders via the TFG Gene
TRPV4-related Disorders via the TRPV4 Gene
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Charcot Marie Tooth Disease via the COX6A1 Gene
Charcot Marie Tooth Type 2U via the MARS Gene
Charcot Marie Tooth Type 4J via the FIG4 Gene
Charcot-Marie-Tooth 1C via the LITAF Gene
Charcot-Marie-Tooth Autosomal Dominant Intermediate C via the YARS Gene
Charcot-Marie-Tooth disease, axonal, type 20, Spinal muscular atrophy with lower extremity predominance and Mental retardation, autosomal dominant type 13 via the DYNC1H1 Gene
Charcot-Marie-Tooth Type 2E/1F via the NEFL Gene
Charcot-Marie-Tooth Type 4D via the NDRG1 Gene
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Familial Dysautonomia via the IKBKAP Gene - Targeted Variants Analysis
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Glycyl tRNA Synthetase-Related Disorders via the GARS Gene
Heat Shock 22 kDa Protein-Related Disorders via the HSPB8 Gene
Heat Shock 27 kDa Protein-Related Disorders via the HSPB1 Gene
Hereditary Motor and Sensory Neuropathy IIB (HMSN2B) via the RAB7A Gene
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Hereditary Sensory Neuropathy, Type IE via the DNMT1 Gene
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Left Ventricular Noncompaction (LVNC) Sequencing Panel with CNV Detection
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CONTACTS

Genetic Counselors
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Citations
  • Auer-Grumbach M. 2008. Orphanet Journal of Rare Diseases. 3: 7. PubMed ID: 18348718
  • Auer-Grumbach M. 2013. Handbook of Clinical Neurology. 115: 893-906. PubMed ID: 23931820
  • Auer-Grumbach M. et al. 2003. Archives of Neurology. 60: 329-34. PubMed ID: 12633143
  • Axelrod FB., Gold-von Simson G. 2007. Orphanet Journal of Rare Diseases. 2: 39. PubMed ID: 17915006
  • Barua M. et al. 2013. Kidney International. 83: 316-22. PubMed ID: 23014460
  • Bird T.D. 2015. Charcot-Marie-Tooth Hereditary Neuropathy Overview. 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: 20301532
  • Bird T.D. 2015. Charcot-Marie-Tooth Neuropathy Type 1. 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: 20301384
  • Boyer O. et al. 2011. Journal of the American Society of Nephrology : Jasn. 22: 239-45. PubMed ID: 21258034
  • Davidson G.L. et al. 2012. Journal of Neurology. 259: 1673-85. PubMed ID: 22302274
  • Drew A.P. et al. 2011. Current Molecular Medicine. 11: 650-65. PubMed ID: 21902652
  • Human Gene Mutation Database (Bio-base).
  • Irobi J. 2004. Human Molecular Genetics. 13: R195-R202. PubMed ID: 15358725
  • Li J. et al. 2013. Molecular Neurobiology. 47: 673-98. PubMed ID: 23224996
  • Rossor A.M. et al. 2013. Nature Reviews. Neurology. 9: 562-71. PubMed ID: 24018473
  • Rossor AM. et al. 2012. Journal of Neurology, Neurosurgery, and Psychiatry. 83: 6-14. PubMed ID: 22028385
  • Rotthier A. et al. 2009. Brain : a Journal of Neurology. 132: 2699-711. PubMed ID: 19651702
  • Saporta A.S. et al. 2011. Annals of Neurology. 69: 22-33. PubMed ID: 21280073
  • van Paassen B.W. et al. 2014. Orphanet Journal of Rare Diseases. 9: 38. PubMed ID: 24646194
  • Zhang F. et al. 2010. American Journal of Human Genetics. 86: 892-903. PubMed ID: 20493460
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.
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