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STAT Comprehensive DMD Test (Sequencing and Deletion/Duplication)

Omics test Model
Test Code D4045F
Test Summary This test analyzes the DMD gene, which is associated with Duchenne and Becker muscular dystrophy.
Turn Around Time 7 - 10 days
Acceptable Sample Types DNA, Isolated , Dried Blood Spots , Saliva , Whole Blood (EDTA)
Acceptable Billing Types Institutional Billing , Self (patient) Payment
NY Approved Yes
Self (patient) Price $1,320.00
Institutional Price $1,320.00
CPT Codes** 81161(x1), 81408(x1)
*TAT starts after the sample and all required sample information is received at the processing laboratory.

**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 testing service has not been cleared or approved by the U.S. Food and Drug Administration. Testing services may not be licensed in accordance with the laws in all countries. The availability of specific test offerings is dependent upon laboratory location.
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Test Code: D4045F
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Test Description

This gene sequencing panel includes both sequencing and deletion/duplication (CNV) analysis for all coding regions of the included genes (unless otherwise noted). All analysis is performed utilizing next-generation sequencing (NGS) technology. All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.

Condition Description

Duchenne and Becker muscular dystrophies are two related conditions that primary affect skeletal muscles which are used for movement and heart muscle. Duchenne and Becker occur almost exclusively in males. Duchenne and Becker muscular dystrophies have similar signs and symptoms and are caused by different mutations in the same gene. Duchenne and Becker muscular dystrophies together affect 1 in 3500 to 5000 newborn males worldwide and are caused by mutations in the DMD gene. Approximately 60% of pathogenic variants in the DMD gene are deletions of one or more exons, approximately 5% are duplications of one or more exons, and approximately 35% are small pathogenic variants within the exon.

Genes

DMD

Test Methods and Limitations

The Agilent Sureselect DMD targeted sequence capture method was used to enrich the entire DMD gene, which includes all exons and introns from this sample’s genomic DNA. DNA was analyzed by next-generation sequencing (NGS) on the Illumina MiSeq or NovaSeq™ 6000 with 2x150 paired-end reads. Primary data analysis is performed using Illumina bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v3.10.8. Tertiary analysis for SNVs is performed using SnpEff v5.0 and Revvity Omics' internal ODIN v1.01.66 software. Deletions and duplications within the DMD gene were assessed using BioDiscovery’s NxClinical v6.1 software (El Segundo, CA). The interpretation of variants is based on our current understanding of the DMD gene. Interpretations may change over time as more information about this gene becomes available. Variants are evaluated by their frequency in databases such as the Genome Aggregation Database (gnomAD), Human Gene Mutation Database (HGMD), and ClinVar. Variants that have a frequency greater than expected given the prevalence of disease are considered to be benign. Benign and likely benign variants are not reported. Intronic variants beyond +/-3 are not reported unless known or suspected to be pathogenic. Some complex variants may not be detected, including complex rearrangements such as inversions or insertions. In some cases, due to the complexity of the sequence, not all variants in the flanking intronic regions are able to be analyzed. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Possible diagnostic errors can include sample mix-ups, genetic variants that interfere with analysis, and other sources. A list of all variants identified in this individual is available upon request.

Detailed Sample Requirements

Whole Blood (EDTA)
Test Details Page
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.
Sample Condition Store at ambient temperature. Do not refrigerate or freeze.
Shipping Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
Special Sample Instructions Clotted or hemolyzed samples are not accepted.
Saliva
Test Details Page
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.
Sample Condition Store at ambient temperature. Do not refrigerate or freeze.
Shipping Ship overnight at ambient temperature.
Special Sample Instructions Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information.
Dried Blood Spots
Test Details Page
Collection Container(s) Dried blood spot card
Collection

Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours.

  • NBS: Please contact Revvity Omics to request the StepOne® kit.
  • Gene Sequencing: Please contact Revvity Omics to request the DBS collection kit.
  • For pre-punched DBS: The required minimum is 6 punches
Sample 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.
DNA, Isolated
Test Details Page
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.
Sample 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 Sample 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 before 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.

Resources

Clinical Genomics Test Requisition Form
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