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Test Code D1305C
Test Summary

Diagnostic whole exome sequencing of the proband and two family member, as well as a biochemical screen of >50 inherited disorders and CNGnome® analysis to detect large copy number changes (CNVs) on the proband

Turn-Around-Time (TAT)* 4 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. CNGnome® analysis will detect CNVs greater than or equal to 25kb throughout the genome and reliably detects chromosome uniparental disomy using low pass genome sequencing (5x). Lastly, 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). Family samples are tested concurrently with the proband sample to further elucidate potential pathogenic changes.

  • 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 v6CREv2 targeted sequence capture method to enrich for the exome. Direct sequencing of the amplified captured regions was performed using 2X100bp 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. Low coverage regions, if any, are limited to ~1% or less of the nucleotides included in this panel unless a pathogenic variant explaining the phenotype is discovered. A list of these regions is available upon request. 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 may be 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. Only CNVs related to phenotype are reported. 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). StepOne: Tandem mass spectrometry as well as other technologies are used for biochemical profiling. CNGnome: Direct sequencing of genomic DNA was performed using 2X150bp reads on Illumina next generation sequencing (NGS) systems at a mean coverage of 5X in the target region. Alignment to the human reference genome (hg19) was performed and copy number variant (CNV) calls made using the NxClinical software v5.0 (BioDiscovery, Inc., El Segundo, CA). CNVs meeting internal quality assessment guidelines are confirmed by real time quantitative PCR (qPCR) for records after results are reported. Some CNVs are confirmed by qPCR before reporting at a director’s discretion. This assay cannot detect CNVs in regions of the genome that are not amenable to NGS and does not interrogate CNVs in mitochondrial DNA. This assay will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), point mutations, methylation abnormalities, genomic imbalances in segmentally duplicated regions and mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Small pathogenic CNVs within the exon, some small intragenic deletions or duplications, as well as complex rearrangements may not be detected. This assay has been validated to detect copy number variants >25 Kb and also has the ability to detect copy number changes such as homozygous deletions. For targeted CNV testing, smaller CNVs may be interrogated, analyzed, and reported per director discretion. This assay may not be able to discern between CNVs that are high copy number gains such as, duplication >=4X. CNVs involving genes with pseudogenes and pseudoexons may not be reliable detected or reported. Due to high similarity of certain regions on chromosome X and chromosome Y, CNVs in the following regions may not be detected for male patients (chrX: 60000-2699520; chrX:154930289-155260560; chrY:10000-2649520; chrY: :59033286-59363566).

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.