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Distal Hereditary Myopathy 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
1351 ANO5 81406 Add to Order
BAG3 81479
CAV3 81404
CRYAB 81479
DES 81405
DNAJB6 81479
DYSF 81408
FHL1 81404
FLNC 81479
GNE 81406
KLHL9 81479
LDB3 81406
MATR3 81479
MYH7 81407
MYOT 81405
SQSTM1 81479
TCAP 81479
TIA1 81479
TTN 81479
VCP 81479
Full Panel Price* $1690.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1351 Genes x (20) $1690.00 81404(x2), 81405(x2), 81406(x3), 81407, 81408, 81479(x11) 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

Many of the subtypes of the distal hereditary myopathies are prevalent only in particular geographic regions. For this reason it is not possible to predict an over-all clinical sensitivity. Analytical sensitivity for the genes in this panel should be high as most pathogenic variants are detectable by this method.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 ANO5$690.00 81479 Add to Order
BAG3$690.00 81479
CAV3$690.00 81479
CRYAB$690.00 81479
DES$690.00 81479
DNAJB6$690.00 81479
DYSF$690.00 81479
FLNC$690.00 81479
GNE$690.00 81479
LDB3$690.00 81479
MATR3$690.00 81479
MYH7$690.00 81479
MYOT$690.00 81479
SQSTM1$690.00 81479
TCAP$690.00 81479
TTN$690.00 81479
VCP$690.00 81479
Full Panel Price* $1290.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (17) $1290.00 81479(x17) 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/duplications are a rare form of pathogenic variation among the genes in this test panel. Therefore clinical sensitivity is predicted to be low.

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Clinical Features

The hereditary distal myopathies are a genetically and clinically heterogeneous group of disorders characterized by prominent weakness beginning in the anterior or posterior compartment of either the distal upper or the distal lower limbs. Weakness of the wrists and ankles is a common pattern of muscle involvement. Age of onset, disease severity, rate of progression, and muscle pathology all vary among the many genetic subtypes of this disorder. For example, patients with Laing myopathy may present as early as 4 years of age (Meredith et al. 2004), while patients affected by Udd myopathy or Welander myopathy may not become clinically affected until the 5th decade of life (Udd et al. 1993; Klar et al. 2013). Serum CpK levels are typically normal or slightly elevated, however, patients with Miyoshi myopathy, Miyoshi-like myopathy, and TCAP related myopathy have CpK levels 100-fold elevated over normal. Muscle pathology of the distal myopathies often reveal varied fiber size and abnormal vacuoles, and those subtypes with myofibrillar changes show accumulation of desmin. A diagnostic algorithm for the distal myopathies using clinical and laboratory data has been proposed (Udd 2009). For a recent review of distal myopathies see Dimachkie and Barohn 2014. 

Genetics

Hereditary distal myopathies can be inherited as autosomal dominant, autosomal recessive, or X linked conditions. The following genes are involved in autosomal dominant distal myopathies: BAG3, CRYAB, DNAJB6, FLNC, LDB3, KLHL9, MATR3, MYOT, TIA1, SQSTM1 and VCP. The following genes are involved in autosomal recessive distal myopathies: ANO5, DYSF, GNE, and TCAP. Some genes can exhibit both dominant and recessive inheritance and include the following: CAV3, DES, MYH7, and TTN.  Scapuloperoneal myofibrillar myopathy (FHL1) is an X-linked dominant disorder. 

See individual gene test descriptions for information on molecular biology of gene products.

Testing Strategy

For this NGS test, the full coding regions, plus ~20 bp of non-coding DNA flanking each exon, are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization method, 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, undocumented and questionable variant calls are confirmed by Sanger sequencing.

This test will cover 98% of the coding exons in the indicated genes plus flanking regions.

This panel does not include coverage of TTN exons 85-95 and exons 153-155 (NM_133378.4). Sanger coverage of these regions is available for an additional charge; however, very few variants have been reported in these regions (Human Gene Mutation Database).

Indications for Test

Individuals with a distal pattern of muscle weakness.

Genes

Official Gene Symbol OMIM ID
ANO5 608662
BAG3 603883
CAV3 601253
CRYAB 123590
DES 125660
DNAJB6 611332
DYSF 603009
FHL1 300163
FLNC 102565
GNE 603824
KLHL9 611201
LDB3 605906
MATR3 164015
MYH7 160760
MYOT 604103
SQSTM1 601530
TCAP 604488
TIA1 603518
TTN 188840
VCP 601023
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Alpha-B Crystallinopathy AD 608810
Autosomal Dominant Limb-Girdle Muscular Dystrophy, Type 1E AD 603511
Distal Myopathy Markesbery-Griggs Type AD 600334
Frontotemporal Dementia and/or Amyotrophic Lateral Sclerosis 3 AD 616437
Inclusion Body Myopathy With Early-Onset Paget Disease And Frontotemporal Dementia AD 167320
Limb-Girdle Muscular Dystrophy, Type 1A AD 159000
Limb-Girdle Muscular Dystrophy, Type 2G AR 601954
Miyoshi Muscular Dystrophy 3 AR 613319
Miyoshi Myopathy AR 254130
Myofibrillar Myopathy, BAG3-Related AD 612954
Myofibrillar Myopathy, Desmin-Related AD,AR 601419
Myofibrillar Myopathy, ZASP-Related AD 609452
Myopathy, Distal, 1 AD 160500
Myopathy, Distal, 2 AD 606070
Myopathy, Distal, 4 AD 614065
Myopathy, Distal, Tateyama Type AD 614321
Myotilinopathy AD 609200
Nonaka Myopathy AR 605820
Scapuloperoneal Myopathy, X-Linked Dominant XL 300695
Spheroid Body Myopathy AD 182920
Welander distal myopathy AD,AR 604454

Related Tests

Name
FHL1-Myopathies via the FHL1 Gene
Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Sequencing Panel
Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia Sequencing Panel
Autosomal Dominant Limb Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Autosomal Dominant Limb-Girdle Muscular Dystrophy, Type 1E (LGMD1E) via the DNAJB6 Gene
Caveolinopathy via the CAV3 Gene
Centronuclear Myopathy Sequencing Panel
Comprehensive Neuromuscular Sequencing Panel
Congenital Cataracts Sequencing Panel
Congenital Fiber Type Disproportion Sequencing Panel
Core Myopathy Sequencing Panel
Dementia Sequencing Panel
Distal Myopathy 2 via the MATR3 Gene
Gnathodiaphyseal Dysplasia via the ANO5 Gene
Hypertrophic Cardiomyopathy and other MYH7-Related Disorders via the MYH7 Gene
Inclusion Body Myopathy-2 (Autosomal Recessive) and Nonaka Myopathy via the GNE Gene
Left Ventricular Noncompaction (LVNC) Sequencing Panel with CNV Detection
Limb Girdle Muscular Dystrophy Type 2B and Miyoshi Myopathy via the DYSF Gene
Limb Girdle Muscular Dystrophy, Type 2J and Tibial Muscular Dystrophy via the TTN Gene (exons 307 - 312)
Limb Girdle Muscular Dystrophy, Type 2L (LGMD2L) and Distal Miyoshi Myopathy (MMD3) via the ANO5 Gene
Limb-Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Long QT Syndrome Sequencing Panel
Myofibrillar Myopathy Sequencing Panel
Myofibrillar Myopathy via the CRYAB Gene
Myofibrillar Myopathy via the DES Gene
Myofibrillar Myopathy via the FLNC Gene
Myofibrillar Myopathy via the LDB3 (ZASP) Gene
Myofibrillar Myopathy, Childhood Onset via the BAG3 Gene
Myotilinopathy via the MYOT Gene
Paget Disease of Bone (PDB) Sanger Sequencing Panel
Paget Disease of Bone via the SQSTM1 Gene
Sialuria via the GNE Gene, Exon 5
Telethoninopathy via the TCAP Gene
Valosin-Containing Protein-Related Disorders via the VCP Gene
Welander Distal Myopathy via the TIA1 Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Dimachkie M.M., Barohn R.J. 2014. Neurologic Clinics. 32: 817-42. PubMed ID: 25037092
  • Klar J. et al. 2013. Human Mutation. 34: 572-7. PubMed ID: 23348830
  • Meredith C. et al. 2004. American Journal of Human Genetics. 75: 703-8. PubMed ID: 15322983
  • Udd B. 2009. Neuromuscular Disorders. 19: 429-38. PubMed ID: 19477645
  • Udd B. et al. 1993. Archives of Neurology. 50: 604-8. PubMed ID: 8503797
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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