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Test Code D0900
Test Summary

CNV analysis utilizing low pass genome sequencing assay (8x).

Turn-Around-Time (TAT)* 10  - 12 days
Acceptable Sample Types
Whole Blood (EDTA)
Dried Blood Spots
DNA, Isolated
Saliva
Acceptable Billing Types
Self (patient) Payment
Institutional Billing
Commercial Insurance
CPT Codes** 81349 (x1)
*TAT starts after the sample and all required sample information is received at PerkinElmer Genomics, or after the benefits investigation is complete if requested for commercial insurance billing.
**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 detects large copy number changes (CNVs) greater than or equal to 25kb throughout the genome and reliably detects chromosome uniparental disomy. Testing is performed utilizing low pass genome sequencing (8x).

  • First-line test for patients with intellectual disability or global developmental delays (Moeschler et al 2014 PMID: 25157020)
  • First-line test for individuals with multiple congenital anomalies (Miller et al. 2010 PMID 20466091)
  • Patients with autism/autism spectrum disorders (ASDs)
  • Patients with suspected chromosomal imbalances including micro-deletion syndromes
  • Suspected uniparental isodisomy
  • Suspected autosomal recessive condition due to close familial relations (consanguinity)
  • Previously negative karyotyping and/or chromosomal microarray results.
  • Determine breakpoints of chromosomal rearrangements previously detected by conventional cytogenetic methods, BAC arrays, and other less sensitive arrays.

Direct sequencing of genomic DNA was performed using 2X150bp reads on Illumina next generation sequencing (NGS) systems at a mean coverage of 8X in the target region. Alignment to the human reference genome (hg19) was performed and copy number variant (CNV) calls made using the NxClinical software v5.1 (BioDiscovery, Inc., El Segundo, CA). CNVs meeting internal quality assessment guidelines are confirmed by real time quantitative PCR (qPCR) for records after results are reported. Some CNVs are confirmed by qPCR before reporting at a director's discretion. This assay cannot detect CNVs in regions of the genome that are not amenable to NGS and does not interrogate CNVs in mitochondrial DNA. This assay will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), point mutations, methylation abnormalities, genomic imbalances in segmentally duplicated regions and mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Small pathogenic CNVs within the exon, some small intragenic deletions or duplications, as well as complex rearrangements may not be detected. This assay has been validated to detect copy number variants >25 Kb and also has the ability to detect copy number changes such as homozygous deletions. For targeted CNV testing, smaller CNVs may be interrogated, analyzed, and reported per director discretion. This assay may not be able to discern between CNVs that are high copy number gains such as, duplication >=4X. CNVs involving genes with pseudogenes and pseudoexons may not be reliable detected or reported. Due to high similarity of certain regions on chromosome X and chromosome Y, CNVs in the following regions may not be detected for male patients (chrX: 60000-2699520; chrX:154930289-155260560; chrY:10000-2649520; chrY: :59033286-59363566).

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.
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.
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.
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.

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