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| Organization: | Alberta Precision Laboratories | ||
| Test Name/Synonym: | Cell-Free DNA Panel, Tumor (Synonyms: Circulating Tumor DNA, cf-DNA, ct-DNA, Plasma DNA, Solid Tumor, Liquid Biopsy, cfDNA and ctDNA) | ||
| Clinical Indications: | Cell-free DNA testing from blood specimens is available for metastatic and castration-resistant prostate cancer patients when archival tumor tissue > 5 years of age, or when archival tumor tissue < 5 years of age but tumor tissue testing has failed or tumor tissue material is not available. | ||
| Collection Alert: | Unopened dedicated tubes are required for molecular testing.
Restricted collection locations: see specimen collection requirements. | ||
| Shipping and Handling Alert: | Transport specimens at room temperature to Molecular Pathology North.
Time sensitive: specimen must be received by Molecular Pathology North within 7 days of collection. | ||
| LABID (Connect Care): | LAB9487 | ||
| Specimen Type: | Blood | ||
| Specimen Source: | Blood | ||
| Primary Container: | 10 mL black and brown top - STRECK Cell-Free DNA BCT® (blood collection tube) | ||
| Minimum Collection Volume: | STRECK: 20.0 mL | ||
| Specimen Collection Requirements: | Collect two full STRECK Cell-Free DNA blood collection tubes. When using a winged blood collection set (butterfly needle) a discard tube must be used if only a Streck Cell-Free DNA blood collection tube is drawn or is the first tube drawn. Order of draw: after the EDTA tube and before the fluoride oxalate tube. Each tube must be full. Collection can only occur at one of the following collection sites: Medicine Hat Regional Hospital - Outpatient Laboratory Chinook Regional Hospital - Outpatient Laboratory Arthur Child Cancer Center - Outpatient Laboratory Red Deer Regional Hospital Centre - Outpatient Laboratory Cross Cancer Institute (CCI) Grande Prairie Regional Hospital - Outpatient Laboratory | ||
| Test Resources: | Submit request using the applicable requisition or Connect Care online order entry:
Please ensure all required information, including patient's clinical history/indication, is provided on the requisition. | ||
| Stability and Storage: | Stable at room temperature. Specimen must be received by Molecular Pathology North within 7 days of collection. | ||
| Processing: | Transport specimens to Molecular Pathology North. Do not centrifuge. Do not aliquot. Do not refrigerate or freeze. Keep specimens at room temperature until ready to transport. | ||
| Transportation: | Transport specimens at room temperature to Molecular Pathology North. | ||
| Method: | Next-Generation Sequencing (NGS) | ||
| Method and Interpretation of Results: | Cell-free DNA extraction from plasma was performed using the Qiagen cfDNA Midi kit. The assay utilizes the Illumina cell-free DNA library Prep kit, IDT for Illumina UMI DNA indexes, and custom oligo probes to target the full coding sequence or hot-spot regions of the following 43 genes: AKT1, AR, ATM, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CDK12, CHEK1, CHEK2, EGFR, EPCAM, ERBB2, ESR1, FANCL, FGFR2, FGFR3, H3-3A, H3-3B, H3C2, H3C3, HOXB13, IDH1, IDH2, KIT, KRAS, MET, MLH1, MSH2, MSH6, NBN, NRAS, PALB2, PDGFRA, PIK3CA, PMS2, PPP2R2A, RAD51B, RAD51C, RAD51D, RAD54L, and TP53 (reference transcripts are listed in the report). Massively parallel sequencing is performed in the Illumina instrument. Base calling, alignment to the reference human genome GRCh37/hg19, unique molecular indexes collapsing of BAM files, and variant calling (single nucleotide variant, small insertion, or small deletion) are generated by the Illumina Dragen bioinformatics pipelines (version 4.0.3). Copy number alterations (CNA) are evaluated using OncoCNV software (version 6.9). Tier I, II, and III variants (per AMP/ASCO/CAP guidelines [1]) present at a minimum of 0.2% variant allele fraction (VAF) for hotspot single nucleotide variants and 0.5% VAF for non-hotspot single nucleotide variants, small insertions or small deletions are reportable. Tier I variants have strong clinical significance with level A and B evidence. Tier II variants have potential clinical significance (level C and D evidence). Tier III variants are variants of unknown clinical significance. Functional assessment of the variants (oncogenicity) follows the ClinGen/CGC/VICC criteria [2]. Test sensitivity is >90% for the detection of single nucleotide variant, small insertion, and small deletion. Current methods may not detect all variants present in the tested genes. When Tier I/II variants are detected in the cell-free DNA, testing of white blood cell DNA of the same blood specimen is performed to determine the somatic versus germline or clonal hematopoiesis of indeterminate potential (CHIP) origin. References: [1] Li M, et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017 Jan;19(1):4-23. [2] Horak P, et al. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genet Med. 2022 May;24(5):986-998. Disclaimer: If the personal or familial history is suspicious for an inherited syndrome, referral to genetic counseling or germline testing (blood or buccal swab specimen) is encouraged. Test results should be interpreted in the context of clinical findings, tumor sampling, and other laboratory data. If the results obtained do not match other clinical or laboratory findings, please contact the laboratory for possible interpretation. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. This assay was validated, and its performance characteristics were determined by the Molecular Pathology Laboratory of Alberta Precision Labs (accredited by the College of Physicians and Surgeons of Alberta). This test is used for clinical purposes and should not be regarded as investigational or for research. | ||
| Routine Turn Around Time: | 3 weeks | ||
| Testing Schedule: | Weekly | ||
| Performing Site: | Molecular Pathology North | ||
| Contact Comments: | Molecular Pathology North: 780-407-6648 | ||
| Last Updated On: | Monday, May 12, 2025 | ||
| Registered Trademark Comments: | STRECK Cell-Free DNA BCT® is a registered trademark of Streck,Inc. | ||
