Analysis and Interpretation of Whole Genome Sequencing External Data

Omics test Model
Test Code D0052
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
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.
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Test Code: D0052
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Test Description

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.

Test Methods and Limitations

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).

Detailed Sample Requirements

Reanalysis Only
Test Details Page
Collection This test is performed on data that has already been generated by Revvity Omics.
Sample Condition N/A
Shipping N/A

Resources

Clinical Genomics Test Requisition Form
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