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WholeCancerTM Panel

Omics test Model
Test Code D5238
Test Summary

This panel analyzes genes associated with hereditary cancer using a genome sequencing-based method, providing full gene sequencing and analysis of targeted genes.
Turn Around Time 4 weeks
Acceptable Sample Types DNA, Isolated , Dried Blood Spots , Saliva , Whole Blood (EDTA)
Acceptable Billing Types Institutional Billing , Self (patient) Payment
NY Approved No
Self (patient) Price $975.00
Institutional Price $1,900.00
CPT Codes** 81479(x2), 81443(x1)
*TAT starts after the sample and all required sample information is received at the processing laboratory.

**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 testing service has not been cleared or approved by the U.S. Food and Drug Administration. Testing services may not be licensed in accordance with the laws in all countries. The availability of specific test offerings is dependent upon laboratory location.
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Test Code: D5238
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Clinical Genomics Test Requisition Form

Test Description

This gene sequencing panel includes both sequencing and deletion/duplication (CNV) analysis for all coding regions of the included genes (unless otherwise noted). All analysis is performed utilizing next-generation sequencing (NGS) technology. All variants are classified according to American College of Genetics and Genomics (ACMG) guidelines.

Indications for Testing

This comprehensive panel includes genes associated with the following hereditary cancers and cancer syndromes:
  • Bloom Syndrome
  • Breast Cancer
  • Carney Complex
  • Costello Syndrome
  • DICER1 Tumor Predisposition Syndrome
  • Familial Meningioma
  • Gastrointestinal and Colorectal Cancers
  • Gynecological Cancers
  • Hereditary Breast and Ovarian Cancer Syndrome
  • Hereditary Thrombocytopenia and Hematologic Cancer Predisposition Syndrome
  • Hyperparathyroidism with Jaw Tumor Syndrome
  • Leukemia
  • Li-Fraumeni Syndrome
  • Lynch Syndrome
  • Melanoma
  • Mismatch Repair Cancer Syndrome
  • Multiple Endocrine Neoplasia 
  • Myelodysplastic Syndrome
  • Neuroblastoma
  • Neurofibromatosis
  • Nevoid Basal Cell Carcinoma Syndrome
  • Nijmegen Breakage Syndrome
  • Non-Small Cell Lung Cancer
  • NTHL1-Deficiency Tumor Predisposition Syndrome
  • Pancreatic Cancer
  • Paraganglioma
  • Perlman Syndrome
  • Peutz-Jeghers Syndrome
  • Pheochromocytoma
  • Pleuropulmonary Blastoma
  • POT1 Tumor Predisposition Syndrome
  • Prostate Cancer
  • PTEN Hamartoma Tumor Syndrome
  • Renal Cancer
  • Retinoblastoma
  • Rhabdoid Tumor Predisposition Syndrome
  • Rothmund-Thomson Syndrome
  • Tuberous Sclerosis
  • Von Hippel-Lindau Syndrome
  • Werner Syndrome
  • Wilms Tumor

Please see professional society guidelines, including the National Comprehensive Cancer Network (NCCN), for the most up-to-date testing criteria.

Genes

AIP, ALK, ANKRD26, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2, DDX41, DICER1, DIS3L2, EGFR, EPCAM, ETV6, EZH2, FANCC, FH, FLCN, GATA2, GPC3, GREM1, HOXB13, HRAS, KIT, LZTR1, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD51C, RAD51D, RB1, RECQL4, RET, RNF43, RUNX1, SAMD9, SAMD9L, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, SRP72, STK11, SUFU, TERC, TERT TMEM127, TP53, TSC1, TSC2, VHL, WRN, WT1

Test Methods and Limitations

Whole genome sequencing is performed on genomic DNA using 2X150bp reads on Illumina next-generation sequencing (NGS) systems at a mean coverage of 40x. A base is considered low coverage at less than 8x. A list of low-coverage regions, if any, is available upon request.

Alignment to the human reference genome (GRCh37) 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. Genes and/or exons located in pseudogene regions are not covered in this assay. 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. 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.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics' internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery's NxClinical v6.1 software.

Detailed Sample Requirements

Dried Blood Spots
Test Details Page
Collection Container(s) Dried blood spot card
Collection

Follow kit instructions. Briefly, allow blood to saturate the card until indicated areas are filled and blood has soaked through the card. Air dry the card at ambient temperature for at least 3 hours.

  • NBS: Please contact Revvity Omics to request the StepOne® kit.
  • Gene Sequencing: Please contact Revvity Omics to request the DBS collection kit.
  • For pre-punched DBS: The required minimum is 6 punches
Sample 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.
DNA, Isolated
Test Details Page
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.
Sample 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 Sample 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 before 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.
Whole Blood (EDTA) (Preferred Sample)
Test Details Page
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.
Sample Condition Store at ambient temperature. Do not refrigerate or freeze.
Shipping Ship overnight at ambient temperature ensuring receipt within 5-days of collection.
Special Sample Instructions Clotted or hemolyzed samples are not accepted.
Saliva
Test Details Page
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.
Sample Condition Store at ambient temperature. Do not refrigerate or freeze.
Shipping Ship overnight at ambient temperature.
Special Sample Instructions Please contact Revvity Omics to request the saliva collection kit for patients who cannot provide a blood sample as whole blood is the preferred sample. Testing using Saliva swabs is currently not available for customers in India. Contact the Revvity Omics laboratory for more information.

Resources

Clinical Genomics Test Requisition Form
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