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STAT Proactive Prenatal Whole Genome Sequencing, Proband ONLY
STAT Proactive Prenatal Whole Genome Sequencing, Proband ONLY
Test code:
D2010HE
STAT Proactive Prenatal Whole Genome Sequencing, Proband ONLY
STAT Whole Genome Sequencing of the fetus.
| Test Code | D2010HE |
|---|---|
| Test Summary |
STAT Whole Genome Sequencing of the fetus. |
| Turn Around Time | 5 - 8 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 |
| Self (patient) Price | $2,850.00 |
|---|---|
| Institutional Price | $3,750.00 |
*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.
**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 code:
D2010HE
Test information
Test description
STAT Prenatal Genome Sequencing includes:
- Mean coverage of 30X or greater with complete coverage of more than 99% of the exome, including over 5,400 disease-associated genes
- Analysis of single nucleotide variants (SNVs), deletions, and duplications in coding and non-coding regions of the genome
- Reliable detection of large-scale copy number variants (CNVs), including microdeletions and other gene- and chromosomal-level events
- Spinal Muscular Atrophy (SMA) screening via SMN1 copy number characterization
All variants are analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines, and pathogenic and likely pathogenic diagnostic variants associated with the submitted phenotype are reported for samples from ongoing pregnancies.
ACMG recommended secondary findings may be requested.
One complimentary reanalysis is included and can be requested at any time.
Access to raw data is included and available via electronic transfer.
Maternal cell contamination (MCC) is offered as a stand-alone test. It is required for testing of samples derived from amniotic fluid and chorionic villi. MCC studies can be requested on other prenatal/fetal samples at the ordering provider's discretion.
Condition description
The purpose of this test is to find the underlying genetic cause for prenatal and/or pediatric-onset findings.
Test methods and limitations
Whole genome sequencing is performed on genomic DNA by short-read next-generation sequencing (NGS). Coverage requirements are based on validation data. An exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered. Revvity Omics has curated deep intronic pathogenic variants from public databases; these are tagged for identification during analysis. Alignment to the human reference genome is performed, and annotated variants are identified. Variants are reviewed based on minimum coverage and alternate allele frequency cut offs defined as per laboratory procedure. Indel and single-nucleotide variants (SNVs) may be confirmed by Sanger sequencing analysis before reporting, based on laboratory requirements. Mitochondrial DNA is sequenced and analyzed using the same pipeline. Genes and/or exons with nonunique sequences, such as those containing pseudogene regions, are not analyzed in this assay.
Copy number variation (CNV) analysis detects deletions and duplications; however, in some instances, due to exon size, sequence complexity, or other factors, certain CNVs may be difficult to detect and analyze. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, or genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; however, possible cases of mosaicism may be detected and reported if laboratory requirements are met.
Primary data analysis is performed using standard FASTQ conversion tools appropriate to the sequencing platform. Secondary analysis is conducted using a high-performance genomic analysis pipeline. Tertiary analysis incorporates established annotation tools together with Revvity Omics' internal software. Copy number variation and absence of heterozygosity assessments are performed using a clinical cytogenomics platform. SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402).
A stand alone Maternal Cell Contamination (MCC) test is required to be completed before the sample is sequenced for WGS.
Detailed sample requirements
Cultured Amniocytes
| SPECIAL SAMPLE INSTRUCTIONS |
Please contact a Revvity Omics Laboratory genetic counselor for information on prenatal test requests and acceptable sample types. |
|---|
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. |
How To Order
Step 1
Choose Your Test
Select the correct test for your patient, and download and fill out the Clinical Genomics test requisition form.
Step 2
Collect Sample
Obtain a sample for testing from the patient using one of the provided Revvity Omics test packs.
Step 3
Send Samples
Send samples and all required forms back to Revvity for processing using pre-paid shipping label.
How can we help you?
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