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STAT Proactive Prenatal Whole Exome Sequencing, QUAD
STAT Proactive Prenatal Whole Exome Sequencing, QUAD
Test code:
D1340HE
STAT Proactive Prenatal Whole Exome Sequencing, QUAD
STAT Healthy Prenatal Whole Exome Sequencing.
| Test Code | D1340HE |
|---|---|
| Test Summary |
STAT Healthy Prenatal Whole Exome Sequencing. |
| Turn Around Time | 7 - 10 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 | $4,700.00 |
|---|---|
| Institutional Price | $4,700.00 |
*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.
This test is not available in your region Japan, please select your nearest laboratory to request more information.
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Test information
Test description
This STAT test is for prenatal use and involves sequencing the whole exome with a mean coverage of 100x, enhanced coverage of known disease-causing genes, and curated deep-intronic variants. The WES test will reliably detect the majority of copy number variations (CNVs) of 3 exons or greater. Smaller CNV events may also be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. The WES assay will also detect microdeletion/duplication events greater than 500kb in clinically relevant regions, although follow-up testing may be warranted to better delineate the exact size of the event and confirm breakpoints. Secondary findings per American College of Medical Genetics (ACMG) recommendations may be requested. Proband only, duo, trio and quad testing options are available, with parental reports included on duo, trio and quad testing if specifically requested.
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.
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
Sequencing is performed on genomic DNA using a targeted sequence capture method to enrich for the exome. Captured regions are directly sequenced on a short-read next-generation sequencing (NGS) system. 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. Alignment to the human reference genome is performed, and annotated variants within the targeted region 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.
This assay cannot detect variants in regions that are not covered, such as deep intronic, promoter, and enhancer regions, or areas containing large numbers of tandem repeats. 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. When reported, copy number variant size is approximate, and 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, 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. A stand alone Maternal Cell Contamination (MCC) test is required to be completed before the sample is sequenced for WGS.
Detailed sample requirements
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. |
|---|
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. |
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.
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