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Test Code D0551
Test Summary

This test provides reanalysis and interpretation of whole exome data previously sequenced at an outside laboratory

Turn-Around-Time (TAT)* 2 - 4 weeks
Acceptable Sample Types
Acceptable Billing Types
Self (patient) Payment
Institutional Billing
*TAT starts after the sample and all required sample information is received at PerkinElmer Genomics, or after the benefits investigation is complete if requested for commercial insurance billing.

This test involves reanalysis and interpretation of previously generated data from an outside laboratory whole exome sequencing test. All variants identified will be analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines. In addition to SNVs, our WES analysis will attempt to reliably detect CNVs of 3 exons or greater. Smaller CNV events may also be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. 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.

Alignment to the human reference genome (hg19) is performed and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Single nucleotide variants (SNVs) meeting internal quality assessment guidelines are confirmed by Sanger sequence analysis for records after results are reported. Indels and SNVs are confirmed by Sanger sequence analysis before reporting at director discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA. Copy number variation (CNV) analysis is designed to detect deletions and duplications of three exons or more; in some instances, due to the size of the exons or other factors, not all CNVs may be analyzed. 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 DRAGEN Bio-IT Platform v.2.03. Secondary and tertiary data analysis is performed using PerkinElmer's internal ODIN v.1.01 software for SNVs and Biodiscovery's NxClinical v.4.3 or Illumina DRAGEN Bio-IT Platform v.2.03 for CNV and absence of heterozygosity (AOH). Genes and/or exons located in pseudogene regions are not covered in this assay. Due to differences in laboratory sequencing protocols and procedures, it is possible that additional limitations will be detected.