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STAT NeoNGS Panel
STAT NeoNGS Panel
STAT NeoNGS Panel
NeoNGS Panel aims to identify newborns with potential childhood onset diseases that have medical managements options, using genomic methodologies. This test can be utilized in both screening and diagnostic settings.
| Test Code | D3200F |
|---|---|
| Test Summary |
NeoNGS Panel aims to identify newborns with potential childhood onset diseases that have medical managements options, using genomic methodologies. This test can be utilized in both screening and diagnostic settings. |
| 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 | No |
| Self (patient) Price | $1,200.00 |
|---|---|
| Institutional Price | $1,750.00 |
**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.
Test information
Test description
This gene sequencing panel includes both sequencing and deletion/duplication (CNV) analysis for all coding regions and 10 base pairs of flanking intronic sequence on both sides of each exon of the included genes (unless otherwise noted). Select pathogenic deep intronic sites may be analyzed. It's important to note that not all variants in the flanking intronic sequence can be reliably assessed due to the sequence's complexity. Copy number variation (CNV) analysis is limited to the genes on this panel. All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.
Indications for testing
Healthy screening or diagnostic testing.
Condition description
The conditions selected for this panel are based on the classic Wilson and Jungner principles for childhood-onset, treatable disorders, as well as our extensive experience in screening the pediatric population (PMID: 37523181). This panel includes early-onset diseases with well-documented gene-disease associations, natural histories, and common differential diagnoses. We also consider targeted treatments, consensus recommendations for long-term surveillance and management, and assess technical feasibility and limitations. The genes in this panel are included and yet differ from those previously published by other researchers (PMID 38585998, 38569677, 38275146) on the utility of genomic newborn screening (gNBS) on childhood-onset genetic diseases. The list will continue to evolve over time as new evidence emerges.
Genes
Test methods and limitations
Sequencing is performed on genomic DNA using a targeted sequence capture method to enrich for the genes of interest. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on next generation sequencing (NGS) systems. 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 on either side are covered at 20X or more. A list of these regions, if any, is available upon request.
Alignment to the human reference genome (GRCh37) 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. Indel and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at director discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA.
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. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions. 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 is performed using bcl2fastq (Illumina) or bases2fastq (Element Biosciences). Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics' internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using Bionano's NxClinical v6.1 software.
Detailed sample requirements
DNA, Isolated
| Collection |
Required DNA Quantity by Test Type*:
|
|---|---|
| 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 |
|
Whole Blood (EDTA)
| 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
| 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
| 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.
|
| 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. |
How To Order
Choose Your Test
Select the correct test for your patient, and download and fill out the Clinical Genomics test requisition form.
Collect Sample
Obtain a sample for testing from the patient using one of the provided Revvity Omics test packs.
Send Samples
Send samples and all required forms back to Revvity for processing using pre-paid shipping label.
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