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Reflex to Whole Genome Sequencing (from genome panels)
Reflex to Whole Genome Sequencing (from genome panels)
Test code:
D5242
Reflex to Whole Genome Sequencing (from genome panels)
Diagnostic whole genome analysis and interpretation of a proband performed after a genome panel test
| Test Code | D5242 |
|---|---|
| Test Summary | Diagnostic whole genome analysis and interpretation of a proband performed after a genome panel test |
| Turn Around Time | 3 - 5 weeks |
| Acceptable Sample Types | Reanalysis Only |
| Acceptable Billing Types | Institutional Billing , Self (patient) Payment |
| NY Approved | No |
| Self (patient) Price | $550.00 |
|---|---|
| Institutional Price | $550.00 |
*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 information
Test description
This test involves a whole genome analysis and interpretation of previously generated data from a qualified Revvity Omics genome panel test. All variants identified will be analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines. In addition to SNVs, our WGS analysis will reliably detect most CNVs. Smaller CNV events may be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. It is recommended that any updated clinical notes and phenotypes are provided to aid in the analysis.
Indications for testing
- Genetically heterogeneous disease caused by likely pathogenic/pathogenic findings in multiple genes
- Condition suggestive of a genetic disorder with a long differential diagnosis list
- Unclear or atypical presentation of a genetic disorder
- Previous genetic testing did not yield a diagnosis
Test methods and limitations
Sequencing is performed on genomic DNA using a targeted sequence capture method to enrich for the exome. Captured regions are 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 cutoffs defined as per laboratory procedure. Indel and single-nucleotide variants (SNVs) may be confirmed by Sanger sequencing analysis before reporting, based on laboratory requirements.
This assay cannot detect variants in regions that are not targeted, including deep intronic, promoter, or enhancer regions. 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 in genes on this panel; 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. Only CNVs identified in genes included in the panel will be reported. 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.
Detailed sample requirements
Reanalysis Only
| Collection |
This test is performed on data that has already been generated by Revvity Omics. |
|---|---|
| Sample Condition |
N/A |
| Shipping |
N/A |
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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