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Core Myopathy 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
1369 MEGF10 81479 Add to Order
MYH7 81407
RYR1 81408
SELENON 81479
TTN 81479
Full Panel Price* $1790.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1369 Genes x (5) $1790.00 81407, 81408, 81479(x3) 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

For autosomal dominant central core disease, pathogenic variants in the RYR1 gene are the major cause and were identified in 40-80% of reported cases (North et al. 2014; Malicdan and Nishino 2007). Dominant MYH7 pathogenic variants are a rare cause, and less than 10 patients have been reported so far (Fananapazir et al. 1993; Clarke et al. 2013). In a few reported cases, RYR1 pathogenic variants lead to autosomal recessive central core disease (North et al. 2014; Malicdan and Nishino 2007). For autosomal recessive minicore myopathy, pathogenic variants in SELENON account for approximately 30%-54% of all affected cases. RYR1-related recessive minicore myoapthy is less common (Beggs and Agrawal. 2003). Only a few cases of TTN and MEGF10 related core myopathies have been reported thus far, and clinical sensitivity is unknown for these genes. 

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 MEGF10$690.00 81479 Add to Order
MYH7$690.00 81479
RYR1$690.00 81479
SELENON$690.00 81479
TTN$690.00 81479
Full Panel Price* $840.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (5) $840.00 81479(x5) 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

Clinical sensitivity is expected to be low because gross deletions and duplications are a rare form of pathogenic variation among the genes of this test panel (Human Gene Mutation Database).

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Clinical Features

Congenital myopathy with cores includes central core disease (CCD) and multiminicore disease (MmD) and is a genetically and clinically heterogeneous disorder (Jungbluth et al. 2011; North et al. 2014). Patients typically present with delayed motor development, generalized muscle weakness, and sometimes scoliosis and respiratory failure. Histopathologically, core myopathies are defined by areas of mitochondria depletion and sarcomere disorganization (cores) on muscle fibers.

Central core disease is a static or slowly progressive myopathy most often caused by dominant variants in the RYR1 gene, and less frequently by MYH7 variants (North et al. 2014). CCD demonstrates a wide range of clinical severity and age of onset, but uniform histopatology. In the newborn period, CCD results in a hypotonic infant with feeding difficulties, respiratory insufficiency, and myopathic facies. Skeletal abnormalities include talipes equinovarus and congenital dislocation of the hips. Childhood-onset CCD presents with mild proximal weakness involving hip and axial muscles and delayed motor development. Skeletal findings such as scoliosis and equinovarus are other complications (Jungbluth et al. 2007). Cases of adult-onset CCD with generally milder clinical symptoms have been described (Duarte et al. 2011). One representative patient had normal arm and leg strength and normal muscle bulk, but was easily fatigued and had difficulty maintaining an upright posture (Jungbluth et al. 2009). Intrafamilial variability of disease severity and pathology is also known (Sewry et al. 2002). Imaging of muscle groups in CCD patients reveals a distinct pattern of involvement (Fischer et al. 2006). The most severely affected muscles are gluteus maximus, medial and anterior compartments of the thigh muscles, and soleus and lateral gastrocnemius muscles of the lower leg.  

Pathogenic variants in the SELENON/SEPN1 gene cause a clinically heterogeneous group of myopathic conditions in which muscle fibers show areas of diminished oxidative staining due to lack of mitochondria (minicores), or fiber-type disproportion in which type 1 muscle fibers are smaller than type 2 fibers. Both minicores and fibertype disproportion can be observed in the muscle of the same patient (Tajsharghi et al. 2005). Approximately 75% of all cases of multiminicore disease (MmD) fall into the classic form with onset at birth or in early childhood (Beggs and Agrawal 2013). Clinical findings include hypotonia, delayed motor development and axial and proximal weakness. Severe, life threatening scoliosis and respiratory complications develop secondary to axial weakness. It is now established that rigid spine muscular dystrophy (RSMD1, Moghadaszadeh et al. 2001) and the severe classic form of MmD are the same entity (Ferreiro et al. 2002). 

In several cases of core myopathy with heart disease, compound heterozygous TTN variants were detected (Chauveau et al 2014). Histopathological results were consistent in exhibiting minicores, abundunct centrally located nuclei, and changes in the internal fiber structure. Despite variability in severity, all patients shared axial muscle weakness (neck flexor weakness and/or scoliosis), distal joint contractures, preserved respiratory function, and primary heart disease.

MEGF10 variants have also been described in patients with a recessive core myopathy characterized by axial and proximal weakness, respiratory impairment, scoliosis, joint contractures, and minicores on muscle biopsy. In one family the presentation was in infancy (Boyden et al 2012), while in another presentation was not until adulthood (Liewluck et al 2016).

Genetics

Core myopathy is a genetically heterogeneous disorder. Pathogenic variants in the RYR1 gene are the most common cause of autosomal dominant CCD (up to 80%) and rarely lead to autosomal recessive CCD (North et al. 2014; Malicdan and Nishino 2007). Dominant MYH7 pathogenic variants in Laing distal myopathy can result in a various pathologies including congenital fiber type disproportion, central cores, and minicores (Fananapazir et al. 1993; Clarke et al. 2013). SELENON-related MmD is inherited as an autosomal recessive disorder, as is RYR1-related minicore myopathy (Beggs and Agrawal 2013). MEGF10 and TTN related core myopathies are both inherited in an autosomal recessive manner (Chauveau et al 2014; Liewluck et al 2016).

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 core myopathy 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.

Of note, this testing includes coverage of the SELENON (NM_20451.2) c.*1107T>C variant in the 3' UTR.

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 clinical and pathological findings consistent with core myopathy.

Genes

Official Gene Symbol OMIM ID
MEGF10 612453
MYH7 160760
RYR1 180901
SELENON 606210
TTN 188840
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
RYR1-Related Congenital Myopathies via the RYR1 Gene
Autosomal Dominant Limb Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Centronuclear Myopathy Sequencing Panel
Comprehensive Neuromuscular Sequencing Panel
Comprehensive Neuropathy Sequencing Panel
Congenital Fiber Type Disproportion Sequencing Panel
Distal Hereditary Myopathy Sequencing Panel
Early-Onset Myopathy, Areflexia, Respiratory Distress, and Dysphagia (EMARDD) via the MEGF10 Gene
Hypertrophic Cardiomyopathy and other MYH7-Related Disorders via the MYH7 Gene
Left Ventricular Noncompaction (LVNC) Sequencing Panel with CNV Detection
Limb Girdle Muscular Dystrophy, Type 2J and Tibial Muscular Dystrophy via the TTN Gene (exons 307 - 312)
Limb-Girdle Muscular Dystrophy (LGMD) Sequencing Panel
Malignant Hyperthermia Susceptibility Sequencing Panel
Selenoprotein N, 1 via the SELENON/SEPN1 Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Beggs A.H., Agrawal P.B. 2013. Multiminicore Disease. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301467
  • Boyden S.E. et al. 2012. Neurogenetics. 13: 115-24. PubMed ID: 22371254
  • Chauveau C. et al. 2014. Human Molecular Genetics. 23: 980-91. PubMed ID: 24105469
  • Clarke N.F. et al. 2013. Neuromuscular Disorders. 23: 432-6. PubMed ID: 23478172
  • Duarte S.T. et al. 2011. Muscle & Nerve. 44: 102-8. PubMed ID: 21674524
  • Fananapazir L. et al. 1993. Proceedings of the National Academy of Sciences of the United States of America. 90: 3993-7. PubMed ID: 8483915
  • Ferreiro A. et al. 2002. American Journal of Human Genetics. 71: 739-49. PubMed ID: 12192640
  • Fischer D. et al. 2006. Neurology. 67: 2217-20. PubMed ID: 17190947
  • Human Gene Mutation Database (Bio-base).
  • Jungbluth H. et al. 2007. Neuromuscular Disorders. 17: 338-45. PubMed ID: 17376685
  • Jungbluth H. et al. 2009. Neuromuscular Disorders. 19: 344-7. PubMed ID: 19303294
  • Jungbluth H. et al. 2011. Seminars in Pediatric Neurology. 18: 239-49. PubMed ID: 22172419
  • Liewluck T. et al. 2016. Muscle & Nerve. 53: 984-8. PubMed ID: 26802438
  • Malicdan M.C.V, Nishino I. 2007. Central Core Disease. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301565
  • Moghadaszadeh B. et al. 2001. Nature Genetics. 29: 17-8. PubMed ID: 11528383
  • North K.N. et al. 2014. Neuromuscular Disorders. 24: 97-116. PubMed ID: 24456932
  • Sewry C.A. et al. 2002. Neuromuscular Disorders. 12: 930–8. PubMed ID: 12467748
  • Tajsharghi H. et al. 2005. Neuromuscular Disorders. 15: 299-302. PubMed ID: 15792869
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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