| Test Code | D5238 | |
| Test Summary | Curated condition-specific panel for hereditary cancer using genome sequencing-based method, providing full gene sequencing and analysis of targeted genes |
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| Turn-Around-Time (TAT)* | 4 weeks | |
| Acceptable Sample Types | Whole Blood (EDTA) DNA, Isolated Dried Blood Spots Saliva |
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| Acceptable Billing Types |
Self (patient) Payment Institutional Billing
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| NY Approved | Yes | |
| Self (patient) Price | $2000.00 | |
| Institutional Price | $2500.00 | |
| CPT Codes** | 81479 (x2), 81443 (x1) |
- 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, including exome sequencing
Whole genome sequencing is performed on genomic DNA using 2X150bp reads on Illumina next-generation sequencing (NGS) systems at a mean coverage of 40X in the target region. 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 are covered at 20X or more. If any, a list of low coverage regions is available upon request. PerkinElmer Genomics has curated deep intronic pathogenic variants in public databases tagged for identification during analysis. 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 the director's discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. This assay does not cover genes and exons located in pseudogene regions. 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 and tandem repeats analysis are performed using Illumina DRAGEN Bio-IT Platform v3.10.8. Secondary and tertiary data analysis is performed using PerkinElmer's internal ODIN v.1.01 software for SNVs and Biodiscovery's NxClinical v.6.1 or Illumina DRAGEN Bio-IT Platform v3.10.8 for CNV and the absence of heterozygosity (AOH). SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402, Genereview: NBK535148).
EDTA (purple top)
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.
Clotted or hemolyzed samples are not accepted.
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.
- 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 spot card
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.
Oragene™ Saliva Collection Kit or ORAcollect-Dx kit
Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer’s 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.