Illumina Microarray Analysis

Illumina Microarray Analysis
WSLH Department: Cytogenetics
WSLH Test Code:890
Includes:High resolution, genome-wide assessment of copy number variants (CNVs) and absence of heterozygosity (AOH).
Methodology:**(CPT Code: 81229)** 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 v4.3 and the GRCh37/hg19 human genome assembly from February 2009. Other databases accessed may include the following: UCSC Genome Browser (http://genome.ucsc.edu/), COSMIC (http://cancer.sanger.ac.uk/cosmic), ClinGen (https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/). Normal limits have been determined by UWCS laboratory validation. Abnormal microarray results may be confirmed by fluorescence in situ hybridization (FISH) or G-banded chromosome analysis. Maternal cell contamination (MCC) may be evaluated when applicable. Parental samples may be requested to interpret the clinical significance of some findings. A portion of this test is run in UWCS facility CLIA#52D2089533 425 Henry Mall, Madison, WI 53706.
Availability:Monday-Friday 7:45 AM - 4:30 PM, Saturday 7:45 AM - 12:00 PM
Turn-around Time:Approximately 14-21 days. (Reports are issued Monday-Friday 7:45 AM - 4:30 PM)
Recommended Uses:The American College of Medical Genetics and Genomics (ACMG) recommends that chromosomal microarray analysis (CMA) is used as a first-line test in the evaluation of individuals with multiple congenital anomalies, non-syndromic intellectual and developmental disability, and autism spectrum disorders.
Contraindications: 
Specimen Requirements:Blood: 4-6 ml Sodium Heparin
Collection Kit/Container: 
Patient Preparation: 
Collection Instructions: 
Specimen Handling and Transport:Draw blood using aseptic techniques into a sterile Sodium Heparin vacuum type tube(s). Invert tube(s) to mix. If using larger tubes, draw to full volume to avoid over-treatment with anticoagulant.
Unacceptable Conditions:Blood that is clotted or hemolyzed is not acceptable. Blood must not be frozen. Plasma and serum are not acceptable.
Requisition Form: 
Required Information:Cytogenetics Lab Genetic Diagnosis Form #131
Results include:With the exception of well-characterized benign copy number variants (CNVs), all CNVs greater than 400-kilobases (kb) will be reported as one of the following categories: likely benign, uncertain, likely pathogenic, or pathogenic. All clinically significant CNVs (uncertain, likely pathogenic, or pathogenic) are reported, regardless of size. Regions of homozygosity (ROH) greater than 20-Megabases (Mb) interstitially or greater than 10-Mb telomerically will be reported as consistent with uniparental disomy (UPD). ROH encompassing 2-10% of the autosomal genome will be reported as Identity by Descent (IBD). ROH encompassing greater than 10% of the autosomal genome will be reported as IBD with a possible familial relationship.
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:High resolution chromosome analysis (Test 801)
Additional Comments:Abnormal or anomalous microarray results may be confirmed by quantitative PCR, FISH, or G-band chromosome analysis prior to the release of final results. Parental samples (if submitted) may be used to interpret the clinical significance of some findings.
Additional Tests Performed: 

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