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Reanalysis and Interpretation of Previous RVTY Whole Genome QUAD Sequencing Test
Reanalysis and Interpretation of Previous RVTY Whole Genome QUAD Sequencing Test
Reanalysis and Interpretation of Previous RVTY Whole Genome QUAD Sequencing Test
This test provides reanalysis and interpretation of sequencing data from a previous whole genome quad test sequenced at Revvity Omics.
| Test Code | D0524 |
|---|---|
| Test Summary |
This test provides reanalysis and interpretation of sequencing data from a previous whole genome quad test sequenced at Revvity Omics. |
| Turn Around Time | 2 - 4 weeks |
| Acceptable Sample Types | Reanalysis Only |
| Acceptable Billing Types | Institutional Billing , Self (patient) Payment |
| NY Approved | Yes |
| CPT Codes** | 81479(x2), 81427(x4), 81460(x1) |
| Self (patient) Price | $950.00 |
|---|---|
| Institutional Price | $950.00 |
**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 test involves reanalysis and interpretation of previously generated data from a Revvity Omics whole genome sequencing 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 CNVs of 3 exons or greater as well as large-scale CNVs such as microdeletions and other gene/chromosomal-level events. CNVs of 1-2 exons may be detected and reported with the recommendation for follow-up testing. Mitochondrial DNA analysis is included. It is recommended that updated clinical notes and phenotypes are provided to aid in the reanalysis.
Test methods and limitations
FASTQ files from a whole genome sequencing test previously completed at Revvity Omics are utilized for reanalysis. 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 low-coverage regions, if any, is available upon request. Revvity Omics has curated deep intronic pathogenic variants in public databases and these are tagged for identification during analysis. 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. Indels and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at the director's discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. Genes and/or exons located in pseudogene regions are not covered in this assay. 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. 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, 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 Illumina bcl2fastq converter v2.19. Secondary analysis and tandem repeats analysis are 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 BioDiscovery’s NxClinical v6.1 software. SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402).
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 |
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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