This test provides reanalysis and interpretation of whole genome data previously sequenced at an outside laboratory.
Test Code | D0052 |
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Test Summary |
This test provides reanalysis and interpretation of whole genome data previously sequenced at an outside laboratory. |
Turn Around Time | 2 - 4 weeks |
Acceptable Sample Types | Reanalysis Only |
Acceptable Billing Types | Institutional Billing , Self (patient) Payment |
NY Approved | No |
This test involves reanalysis and interpretation of previously generated data from an outside laboratory 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 attempt to 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.Due to differences in laboratory sequencing protocols and procedures, it is possible that additional limitations will be detected. It is recommended that updated clinical notes and phenotypes are provided to aid in the reanalysis.
Whole genome sequencing is performed by an external laboratory and the FASTQ files are provided directly to Revvity Omics. 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. 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 (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. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. The external FASTQ data is analyzed 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).
Collection |
This test is performed on data that has already been generated by Revvity Omics. |
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Sample Condition |
N/A |
Shipping |
N/A |
Select the correct test for your patient, and download and fill out the Clinical Genomics test requisition form.
Obtain a sample for testing from the patient using one of the provided Revvity Omics test packs.
Send samples and all required forms back to Revvity for processing using pre-paid shipping label.
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