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First Reanalysis on Previous RVTY Whole Genome Sequencing Test
First Reanalysis on Previous RVTY Whole Genome Sequencing Test
First Reanalysis on Previous RVTY Whole Genome Sequencing Test
This test provides a single complementary reanalysis and interpretation of whole genome data previously sequenced at Revvity Omics
| Test Code | D0590 |
|---|---|
| Test Summary |
This test provides a single complementary reanalysis and interpretation of whole genome data previously sequenced at Revvity Omics |
| Turn Around Time | 2 - 4 weeks |
| Acceptable Sample Types | Reanalysis Only |
| NY Approved | Yes |
*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.
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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
Whole genome sequencing is performed on genomic DNA using 2X150bp reads on Illumina next-generation sequencing (NGS) systems at a mean coverage of 40X in the target region. 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 are covered at 20X or more. If any, a list of low coverage regions is available upon request.
Revvity Omics has curated deep intronic pathogenic variants in public databases tagged for identification during analysis. Alignment to the human reference genome (hg19) 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.
This assay does not cover genes and exons located in pseudogene regions. 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 and tandem repeats analysis are performed using Illumina DRAGEN Bio-IT Platform v.3.4.12. Secondary and tertiary data analysis is performed using Revvity Omics' internal ODIN v.1.01 software for SNVs and Biodiscovery's NxClinical v.6.1 or Illumina DRAGEN Bio-IT Platform v.3.4.12 for CNV and the absence of heterozygosity (AOH). SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402, Genereview: NBK535148).
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
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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