CNGnome NGS Array

Omics test Model
Test Code D0900
Test Summary

CNV analysis utilizing low pass genome sequencing assay (8x).
Turn Around Time 10 - 12 days
Acceptable Sample Types DNA , Dried Blood Spots , Saliva , Whole Blood (EDTA)
Acceptable Billing Types Institutional Billing , Self (patient) Payment
NY Approved No
Self (patient) Price $725.00
Institutional Price $1,000.00
CPT Codes** 81349(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: D0900
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Test Description

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).

Indications for Testing

  • 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 disorder (ASD)
  • 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

Test Methods and Limitations

Direct sequencing of genomic DNA was performed using 2X150bp reads on Illumina next generation sequencing (NGS) systems at a mean coverage of 10X in the target region. Alignment to the human reference genome (GRCh37) was performed and copy number variant (CNV) calls made using the NxClinical software v6.1 (BioDiscovery, Inc., El Segundo, CA). CNVs meeting internal quality assessment guidelines may be confirmed by alternative assays 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. CNVs involving genes with pseudogenes and pseudoexons may not be reliably detected or reported. This assay will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), point mutations, 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. This assay may not be able to detect small pathogenic CNVs within an exon, small intragenic deletions or duplications, and complex rearrangements. This assay may not be able to accurately quantify copy number state equal to or greater than 4 (triplication or above). Due to high sequence similarity between the pseudoautosomal regions (PARs) of the X and Y chromosomes, CNVs located within these genomic segments (chrX:60000-2699520; chrX:154930289-155260560; chrY:10000-2649520; chrY:59033286-59363566) cannot be accurately localized to either the X or Y chromosome in male individuals.

Detailed Sample Requirements

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.
Whole Blood (EDTA) (Preferred Sample)
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.

Resources

Clinical Genomics Test Requisition Form
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