| Test Code | D5241 | |
| Test Summary | Curated condition-specific panel for muscular dystrophy using genome sequencing-based method, providing full gene sequencing and analysis of targeted genes |
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| Turn-Around-Time (TAT)* | 4 weeks | |
| Acceptable Sample Types | Whole Blood (EDTA) DNA, Isolated Dried Blood Spots Saliva |
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| Acceptable Billing Types |
Self (patient) Payment Institutional Billing
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| Self (patient) Price | $2000.00 | |
| Institutional Price | $2500.00 | |
| CPT Codes** | 81479 (x2), 81312 (x1), 81443 (x1) |
*TAT starts after the sample and all required sample information is received at PerkinElmer Genomics.
**The CPT codes listed are in accordance with Current Procedural Terminology, a publication of the American Medical Association, and are provided for informational purposes only. CPT coding is the sole responsibility of the billing party.
This test involves sequencing expertly curated genes using a genome sequencing test platform with mean coverage of 40X and phenotypically driven variant analysis to minimize variants of uncertain significance (VUS). All variants identified will be analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines. This test includes the reliable detection of deletions, duplications, and other gene- and chromosomal-level events. Mitochondrial DNA analysis is included.
- Genetically heterogeneous disease caused by likely pathogenic/pathogenic findings in multiple genes
- Condition suggestive of a genetic disorder with a long differential diagnosis list
- Unclear or atypical presentation of a genetic disorder
- Previous genetic testing did not yield a diagnosis, including exome sequencing
This panel may help identify or be used for a better understanding of the following conditions:
- Congenital Muscular Dystrophies
- Dystroglycanopathy
- Dystrophinopathy
- Emery-Dreifuss muscular dystrophy
- Epidermolysis bullosa simplex with muscular dystrophy
- Facioscapulohumeral muscular dystrophy 2
- Glycogen storage disease type II, Pompe disease
- LAMA2-related muscular dystrophy
- Limb-Girdle muscular dystrophy
- Myotonic dystrophy
- Neutral lipid storage disease with myopathy
- Oculopharyngeal muscular dystrophy
ANO5, B3GALNT2, B4GAT1, BVES, CAPN3, CAV3, CHKB, CNBP, COL12A1, COL6A1, COL6A2, COL6A3, CRPPA, DAG1, DES, DMD, DMPK, DNAJB6, DOK7, DPM1, DPM2, DPM3, DYSF, EMD, FHL1, FKRP, FKTN, GAA, GMPPB, HNRNPDL, INPP5K, ITGA7, LAMA2, LARGE1, LIMS2, LMNA, MYOT, PABPN1, PLEC, PNPLA2, POGLUT1, POMGNT1, POMGNT2, POMK, POMT1, POMT2, RXYLT1, SELENON, SGCA, SGCB
This test contains more than 50 genes. Click here to view the complete list.
Whole genome sequencing is performed on genomic DNA using 2X150bp reads on Illumina next-generation sequencing (NGS) systems at a mean coverage of 40X in the target region. A base is considered to have sufficient coverage at 20X, and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence are covered at 20X or more. If any, a list of low coverage regions is available upon request. PerkinElmer Genomics has curated deep intronic pathogenic variants in public databases tagged for identification during analysis. Alignment to the human reference genome (hg19) is performed, and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indels and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at the director's discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. This assay does not cover genes and exons located in pseudogene regions. Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be analyzed or may be difficult to detect. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis and tandem repeats analysis are performed using Illumina DRAGEN Bio-IT Platform v3.10.8. Secondary and tertiary data analysis is performed using PerkinElmer's internal ODIN v.1.01 software for SNVs and Biodiscovery's NxClinical v.6.1 or Illumina DRAGEN Bio-IT Platform v3.10.8 for CNV and the absence of heterozygosity (AOH). SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402, Genereview: NBK535148).
Whole Blood (EDTA) (Preferred sample type)
Collection Container(s):
EDTA (purple top)
Collection:
Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.
Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
SPECIAL INSTRUCTIONS
Clotted or hemolyzed samples are not accepted.
Clotted or hemolyzed samples are not accepted.
DNA, Isolated
Collection:
Required DNA Quantity by Test Type*:
- Next Generation Sequencing (NGS): Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA.
- Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested).
- Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.
Condition: * Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met.
Shipping: Ship overnight at ambient temperature.
SPECIAL INSTRUCTIONS
- Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results.
- Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor prior to submitting a DNA sample from any non-CLIA certified laboratory.
- Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.
Dried Blood Spots
Collection Container(s):
Dried blood spot card
Collection:
Follow kit instructions. Briefly, allow blood to saturate card until indicated areas are filled and blood has soaked through card. Air dry card at ambient temperature for at least 3 hours.
- NBS: Please contact PKIG to request the StepOne® kit.
- Gene Sequencing: Please contact PKIG to request the DBS collection kit.
- For pre-punched DBS: The required minimum 6 punches with 3.2 mm or 4 punches 4.75 mm.
Condition: Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer.
Shipping: Follow kit instructions. Double bag and ship overnight at ambient temperature.
Saliva
Collection Container(s):
Oragene™ Saliva Collection Kit or ORAcollect-Dx kit
Collection:
Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer’s instructions.
Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature.
SPECIAL INSTRUCTIONS
Please contact PerkinElmer to request the saliva collection kit for patients that cannot provide a blood sample as whole blood is the preferred sample.
Please contact PerkinElmer to request the saliva collection kit for patients that cannot provide a blood sample as whole blood is the preferred sample.