Illumina Microarray Analysis - Oncology

Illumina Microarray Analysis - Oncology
WSLH Department: Cytogenetics
WSLH Test Code:890ONC
Includes:High resolution, genome-wide assessment of copy number variants (CNVs) and copy neutral loss of heterozygosity (cn-LOH).
Methodology:**(CPT Code: 81406)** 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.
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.
Specimen Requirements:1-3 mL bone marrow collected in sodium heparin OR 3-5 mL whole blood collected in sodium heparin or EDTA.
Collection Kit/Container: 
Patient Preparation: 
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.
Specimen Handling and Transport:Refrigerate until time of shipment. Ship sample at room temperature for receipt within 24 hours.
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).
Limitations:This assay will not detect point mutations or balanced alterations (reciprocal translocations, Robertsonian translocations, inversions and insertions), imbalances smaller than the resolution of this array, or low level mosaicism (less than 20%).
Additional Tests Recommended:G-banded chromosome analysis, fluorescence in situ hybridization (FISH) analysis
Additional Comments: 
Additional Tests Performed: 

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