Illumina Microarray Analysis - Oncology Print

WSLH Department: Cytogenetics
WSLH Test Code: 890ONC
Availability: Monday-Friday 7:45 AM - 4:30 PM, Saturday 7:45 AM - 12:00 PM
Turn-around Time: 4-8 days
Recommended Uses: Illumina Microarray Analysis Oncology is recommended for individuals with a new diagnosis or suspected diagnosis of a hematological disease, or individuals with relapsed disease. The results are intended for use by the physician to further refine diagnoses, offer more accurate prognostic assessments and select optimal treatments.
Contraindications: Not recommended for minimal residual disease monitoring or for individuals with expected lower levels of malignant cells.
Additional Tests Performed:
Patient Preparations:
Specimen Requirements: 1-3 mL bone marrow collected in sodium heparin OR 3-5 mL whole blood collected in sodium heparin or EDTA.

DNA: 3-5 ug DNA in TE buffer at a concentration of 50-100 ng/uL. For best results, DNA should be treated with RNAse. DNA must be extracted in a CLIA-certified Laboratory OR a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS.
Specimen Handling & Transport: Refrigerate until time of shipment. Ship sample at room temperature for receipt within 24 hours.
Collection Kit/Container:
Collection Instructions: Bone marrow: Draw sodium heparin solution (1000 USP units/ml) into the syringe to be used for aspiration and then expel (over-heparinization is toxic to the cells). Transfer 1-3 mL bone marrow to a sterile, sodium heparin vacuum tube.

Blood: Draw blood using aseptic techniques into a sterile sodium heparin or EDTA vacuum tube. Invert tube to mix. If using larger tubes, draw to full volume to avoid over-treatment with heparin.

DNA: DNA extracted from peripheral blood, cord blood, buccal swab, saliva, fresh and frozen tissue (prenatal and postnatal), bone marrow. We DO NOT accept DNA from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue. Label with the patient name plus a second identifier. DNA concentration and volume must also be provided on the specimen label.
Unacceptable Conditions: Bone marrow/Blood that is clotted or hemolyzed is not acceptable. Bone marrow/Blood must not be frozen. Plasma and serum are not acceptable.
Requisition Form: Cytogenetics Lab Neoplasia Diagnosis Form #132
Required Information: Cytogenetics Lab Neoplasia Diagnosis Form #132
Results Include: Copy number variants (CNVs) are reported when found to have clear or suspected clinical relevance; CNVs which correspond to benign variants frequently observed in the general population are not reported. Long stretches of homozygosity will only be reported if they most likely represent somatic events in tumor cells, or when their size exceeds 5-Megabases (Mb).

Variant Classification Tier System (PMID:31138931):

Tier 1: Variants with strong diagnostic, prognostic, and/or therapeutic clinical significance. Tier 1A includes acquired variants that define a specific entity in the WHO classification, are included in professional guidelines, can be treated by a targeted FDA approved drug, or germline pathogenic variants associated with cancer predisposition. Tier 1B includes acquired variants or a certain pattern of acquired variants with strong high-quality evidence in the literature, including well-powered studies with expert consensus.

Tier 2: Acquired variants with some clinical significance. They include recurrent variants observed in different neoplastic disorders but are not specific or variants with possible clinical significance as shown in small studies. They usually encompass COSMIC cancer genes(s).

Tier 3: Acquired clonal variants with no documented neoplastic disorder association. All variants that don't meet the criteria for tiers 1 and 2 and cannot be classified as benign or likely benign, can be classified as tier 3 variants.

Tier 4: Benign or likely benign variants that don't encompass COSMIC cancer gene(s) and are listed in the ClinGen curated benign variants or in the DGV with >1% population frequency.
Limitations: This assay will detect aneuploidy, deletions, and/or duplications of represented loci, but will not detect point mutations or balanced alterations (reciprocal translocations, Robertsonian translocations, inversions and insertions). The assay is currently validated for the detection of copy number changes greater than 52-kb in size (smaller changes may be detected depending on gene content and probe number) and loss of heterozygosity greater than 3-Mb (smaller regions may be detected depending on gene content and probe number). Based on the results of internal validation studies, abnormalities present in a mosaic state are reliably detected if the mosaicism level (percentage of abnormal cells) is 20% or higher. The failure to detect an alteration at any locus does not exclude all anomalies at that locus.
Additional Tests Recommended: G-banded chromosome analysis, fluorescence in situ hybridization (FISH) analysis
Additional Comments:
Methodology: Isolated genomic DNA is quantified, amplified, fragmented, and hybridized to the Illumina CytoSNP850K bead chip that contains 850,000 different locus-specific 50-mer probes with at least 15x redundancies. The 850,000 probes have an average probe spacing of 1.8 kilobases (kb) across the whole genome (backbone coverage) and increased probe spacing (1 kb) in targeted cytogenetically relevant genes. The minimum functional resolution of a CNV is 36 kb across the genome and 20 kb in targeted regions. The minimum functional resolution of LOH is 900 kb. Fluorescence type and intensity of each probe is analyzed by Illumina's Genome Studio and BlueFuse software. Data analysis is performed using BlueFuse v4.1 and the GRCh37/hg19 human genome assembly from February 2009.
Includes: High resolution, genome-wide assessment of copy number variants (CNVs) and copy neutral loss of heterozygosity (CN-LOH).
CPT Code: 81277
Price: For pricing information, please call 608-262-0402.
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