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Test Code D1005
Test Summary

Diagnostic whole exome sequencing with a biochemical screen of >50 inherited disorders in the proband only

Turn-Around-Time (TAT)* 4 - 6 weeks
Acceptable Sample Types
Dried Blood Spots
Whole Blood (EDTA)
Acceptable Billing Types
Self (patient) Payment
Institutional Billing
Commercial Insurance
*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 sequencing of the whole exome with a mean coverage of 100x, enhanced coverage of known disease-causing genes, and curated deep-intronic variants. Our WES test will reliably detect the majority of copy number variations (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. The WES assay will also detect microdeletion/duplication events greater than 500kb in clinically relevant regions, although follow-up testing may be warranted to better delineate the exact size of the event and confirm breakpoints. A comprehensive biochemical profile is performed to identify the presence of more than 50 inherited disorders, the full core and secondary panel recommended by the American College of Medical Genetics. This includes conditions that may not be included in state-mandated programs. In addition to the primary analysis, patients can opt-in to a comprehensive secondary analysis including the recommended list by the American College of Medical Genetics and Genomics (ACMG).

  • 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

Whole exome sequencing is performed on genomic DNA using the Agilent SureSelect Clinical Research Exome v3 targeted sequence capture method to enrich for the exome. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on Illumina next generation sequencing (NGS) systems. 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. 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 director discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. Mitochondrial variants are reported at a minimum of 5% heteroplasmy if the average coverage of the mitochondrial genome is 1000x. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter, and enhancer regions, and areas containing large numbers of tandem repeats. Genes and/or exons located in pseudogene regions are not covered in this assay. 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 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 is performed using Illumina DRAGEN Bio-IT Platform v.3.4.12. Tertiary data analysis is performed using SnpEff v4.3t and PerkinElmer’s internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v5.1 software.

StepOne® biochemical assay consists of tandem mass spectrometry as well as other technologies are used for biochemical profiling.

Dried Blood Spots (Preferred sample type)
Collection Container(s): Dried blood spot card
Collection: Follow kit instructions. Briefly, allow blood to saturate card until indicated areas are filled and blood has soaked through card. Air dry card at ambient temperature for at least 3 hours.
  • NBS: Please contact PKIG to request the StepOne® kit.
  • Gene Sequencing: Please contact PKIG to request the DBS collection kit.
Shipping: Follow kit instructions. Double bag and ship overnight at ambient temperature.
Whole Blood (EDTA)
Collection Container(s):

EDTA (purple top)

Collection:

Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: 5 to 10 mL Southern Blot Analysis requires 3 mL blood.

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature ensuring receipt within 4-days of collection.
SPECIAL INSTRUCTIONS
Clotted or hemolyzed samples are not accepted.