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Test Code D1301
Test Summary

Diagnostic whole exome sequencing of the proband and two family members, with additional healthy analysis and interpretation performed on the family members.

Turn-Around-Time (TAT)* 4 - 6 weeks
Acceptable Sample Types
Whole Blood (EDTA)
DNA, Isolated
Dried Blood Spots
Saliva
Acceptable Billing Types
Self (patient) Payment
Institutional Billing
Commercial Insurance
CPT Codes** 81416 (x1), 81415 (x1), 81460 (x1), 81479 (x2)
*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.
**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 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. 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. Family members’ reports with secondary findings are generated. Please note, appropriate selection must be made on the test requisition form as well as the consent form in order to generate family members’ reports.

  • 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.

Whole Blood (EDTA) (Preferred sample type)
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: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
SPECIAL INSTRUCTIONS
Clotted or hemolyzed samples are not accepted.
DNA, Isolated
Collection:

Required DNA Quantity by Test Type*:

  • Next Generation Sequencing (NGS): Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA.
  • Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested).
  • Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.

 

Condition: * Required DNA Quality: High molecular weight DNA (>12kb). A260/A280 reading should be ≥ 1.8. A260/230 a ratio range of 1.8 to 2.2. Contact the laboratory for specific amounts if total ng cannot be met.
Shipping: Ship overnight at ambient temperature.
SPECIAL INSTRUCTIONS
  • Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results.
  • Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor prior to submitting a DNA sample from any non-CLIA certified laboratory.
  • Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.
Dried Blood Spots
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.
  • For pre-punched DBS: The required minimum 6 punches with 3.2 mm or 4 punches 4.75 mm.
Condition: Follow the instructions provided with the collection set. Store the dried blood at ambient temperature for up to two days. If the specimen cannot be sent as soon as it is dry, the filter paper should be placed in a sealable plastic bag and stored in a refrigerator (≤ 8°C) or preferably in a freezer.
Shipping: Follow kit instructions. Double bag and ship overnight at ambient temperature.
Saliva
Collection Container(s):

Oragene™ Saliva Collection Kit or ORAcollect-Dx kit

Collection:

Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer’s instructions. 

Condition: Store at ambient temperature. Do not refrigerate or freeze.
Shipping: Ship overnight at ambient temperature.
SPECIAL INSTRUCTIONS
Please contact PerkinElmer to request the saliva collection kit for patients that cannot provide a blood sample as whole blood is the preferred sample.

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