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STAT Prenatal CNGnome NGS Array
STAT Prenatal CNGnome NGS Array
STAT Prenatal CNGnome NGS Array
STAT prenatal CNV analysis utilizing low pass genome sequencing Assay (8x).
| Test Code | D0900E |
|---|---|
| Test Summary |
STAT prenatal CNV analysis utilizing low pass genome sequencing Assay (8x). |
| Turn Around Time | 10 - 12 days |
| Acceptable Sample Types | Cultured Amniocytes , Cultured Chorionic Villi , DNA, Isolated , Products of Conception |
| Acceptable Billing Types | Institutional Billing , Self (patient) Payment |
| NY Approved | No |
| CPT Codes** | 81349(x1) |
**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 information
Test description
This STAT prenatal test detects large copy number changes (CNV) greater than or equal to 25kb throughout the genome and reliably detects chromosome uniparental disomy. Testing is performed utilizing low pass genome sequencing (8x).
Maternal cell contamination (MCC) is offered as a stand-alone test and is required to accompany prenatal testing for samples derived from amniotic fluid, and chorionic villi sampling. MCC study can be requested on other prenatal / fetal samples at the ordering provider's discretion.
Indications for testing
- Abnormal NIPT result
- Abnormal maternal serum screen
- Advanced maternal age
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 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).
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 |
|
Cultured Chorionic Villi
| Collection Container(s) |
Two T-25 flasks |
|---|---|
| Collection |
All prenatal specimens will be tested for maternal cell contamination (MCC). Send maternal blood (EDTA tube) for comparison. If blood is unavailable, we will accept genomic DNA and Saliva sample types. |
| Sample Condition |
Transfer cultured amniocytes or cultured CVS to two T-25 flasks at ≥80% confluence. |
| Shipping |
Cultures topped off with sterile medium and shipped immediately at ambient temperature by overnight express with arrival Monday-Friday only. |
| SPECIAL SAMPLE INSTRUCTIONS |
For prenatal samples, Revvity Omics will provide a shipping label to use for shipping the sample to our lab. Please call 1 (866) 354-2910 to arrange this. At this time, you will also be connected to a laboratory genetic counselor to answer any questions about the testing. For samples originating outside of the United States, please contact your nearest Revvity Omics laboratory for more information. |
Products of Conception
| Collection Container(s) |
Sterile, screw-top container filled with tissue culture transport medium. |
|---|---|
| Collection |
All prenatal specimens will be tested for maternal cell contamination (MCC). Send maternal blood (EDTA tube) for comparison. Transport products of conception and/or fresh tissue (minimum: 10 mg) in a sterile, screw-top container filled with tissue transport medium. Do not place in formalin. If the specimen is too large for a normal collection tube, a larger sterile container can be used. |
| Sample Condition |
If the autopsy is performed: Facia lata, diaphragm, tendon, skin, tissue from internal organs (if fresh), chest wall cartilage (particularly if macerated), or placenta from fetal side. If no autopsy is performed: Placenta from fetal side is preferred, e.g., villi. Umbilical cord is also acceptable. State clearly in the TRF whether the tissue was of fetal or placental in origin. |
| Shipping |
Shipped immediately at ambient temperature or with a cold pack, especially under hot weather to the laboratory by overnight express with arrival Monday-Friday only. Alternatively, fresh POC and/or tissue samples can be snap-frozen and kept at -80°C. Frozen tissue samples should be shipped overnight on dry ice with arrival Monday-Friday only - NO WEEKEND SHIPMENTS! |
| SPECIAL SAMPLE INSTRUCTIONS |
For prenatal samples, Revvity Omics will provide a shipping label to use for shipping the sample to our lab. Please call 1 (866) 354-2910 to arrange this. At this time, you will also be connected to a laboratory genetic counselor to answer any questions about the testing. For samples originating outside of the United States, please contact your nearest Revvity Omics laboratory for more information. |
Cultured Amniocytes
| SPECIAL SAMPLE INSTRUCTIONS |
Please contact a Revvity Omics Laboratory genetic counselor for information on prenatal test requests and acceptable sample types. |
|---|
Resources
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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