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Reflex to Whole Genome Sequencing (from genome panels)

Omics test Model
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.

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

Molecular testing includes whole genome sequencing, copy number variant analysis, mitochondrial genome sequencing, repeat expansion disorder screening, and deletion analysis for spinal muscular atrophy (SMA). FASTQ files from previous sequencing test are utilized. 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
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