Illumina Microarray Analysis

Illumina Microarray Analysis
WSLH Department: Cytogenetics
WSLH Test Code:890
CPT Code:81229
Price:For pricing information, please call 608-262-0402.
Includes:High resolution, genome-wide assessment of copy number variants (CNVs) and absence of heterozygosity (AOH).
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 v4.4 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/), Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home), and DECIPHER (https://decipher.sanger.ac.uk/). 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.
Availability:Monday-Friday 7:45 AM - 4:30 PM, Saturday 7:45 AM - 12:00 PM
Turn-around Time:Prenatal/infant (0-1 year): approx. 7-10 days; Children >1 year, adult, and products of conception: approx. 12-21 days, with an average of 12 days (Reports 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.

The American College of Obstetricians and Gynecologists recommends CMA in patients with a fetus with a structural abnormality detected by ultrasound and in cases of intrauterine fetal demise or stillbirth.
Contraindications: 
Specimen Requirements:Blood (including cord blood): 4-6 ml Sodium Heparin
Skin biopsy: 1-2mm punch biopsy
Saliva: Isohelix Saliva Collection kit used according to manufacturer instructions
Amniotic fluid: 15-30ml amniotic fluid
Chorionic Villus Sampling: 10mg chorionic villi
Tissue, including products of conception: 0.3-0.5cm cubed section of each tissue
Collection Kit/Container:Prenatal specimens: Cytogenetics and Molecular Genetics Collection Kit, Saliva: Isohelix Saliva Collection kit
Patient Preparation: 
Collection Instructions:Blood: 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.

Saliva: Collect according to manufacturer instructions.

Amniotic Fluid: Collect amniotic fluid under sterile, ultrasound guided conditions using a 22-gauge needle inserted through the uterine wall and into the amniotic cavity. Discard the first 1-2ml of amniotic fluid to minimize the possibility of maternal cell contamination. Dispense amniotic fluid into a sterile 15 ml centrifuge tube.

For skin biopsies: Skin should be cleaned using alcohol, do not use iodine or betadine as these will compromise the cell growth in culture. Do a 1-2mm punch biopsy that goes full depth through the epidermis into the sub-cutaneous fat. Place the specimen in a sterile tissue vial containing transport media.

For chorionic villus sample: Using aseptic technique, obtain at least 10mg of chorionic villi, taken between 9-38 weeks of gestation. Place villi into a flask with transport media provided by the department.

For products of conception specimens: Healthy tissue is pale pink to red in color, indicating an active blood supply. Placenta that includes chorionic villi is usually mottled pink/red. Samples that are solid dark red are usually blood clots and may not contain fetal tissue. Tissue that is pale tan to brown should be avoided if possible as this indicates necrosis. A 0.3-0.5cm cubed section of each tissue type should be collected using aseptic procedures. Place the specimen in a sterile tissue vial containing transport media. If multiple tissues are sent, please place the placenta in one vial and the other tissue(s) in a separate vial to minimize contamination of the tissues.
Specimen Handling and Transport:Store and transport specimens at room temperature (may be transported with coolant during hot weather, >85 degrees F). DO NOT FREEZE. The laboratory must receive specimens within 24-48 hours of collection.
Unacceptable Conditions:Blood that is clotted or hemolyzed is not acceptable. Blood must not be frozen. Plasma and serum are not acceptable.

Chorionic villus sample: A specimen with no fetal material identified and only maternal decidua present will be rejected.
Requisition Form: 
Required Information:Cytogenetics Lab Genetic Diagnosis Form #131

Please include phenotype forms:
Prenatal:
http://www.slh.wisc.edu/wp-content/uploads/2013/10/WSLHprenatalphenotypeform.pdf

Postnatal:
http://www.slh.wisc.edu/wp-content/uploads/2013/10/WSLHpostnatalphenotypeform.pdf
Results include:Copy number variant classification follows on ACMG guidelines (PMID: 31690835). All copy number variants (CNVs) within the limit of detection classified as pathogenic or likely pathogenic will be reported, regardless of size. This includes secondary/incidental findings and probable carrier status (see definitions below). CNVs of uncertain clinical significance and likely benign CNVs will be reported if greater than 400 kilobases. Smaller CNVs (less than 400 kilobases) of uncertain significance may be reported based on criteria such as genomic content, published literature, public databases and internal lab data, and inheritance pattern/family history.

Regions of homozygosity (ROH) greater than 5 Megabases (Mb) telomerically, 10 Mb interstitially on imprinted chromosomes (6, 7, 11, 14, 15, 20) or 15 Mb interstitially on non-imprinted chromosomes will be reported as consistent with uniparental disomy (UPD). ROH encompassing 2-10% of the autosomal genome will be reported as excess homozygosity. ROH encompassing greater than 10% of the autosomal genome will be reported as excess homozygosity with a possible familial relationship.

Secondary/Incidental findings: These represent copy number variants that are unrelated to the patient’s stated reason for referral, but have clear medical relevance for the patient’s care.
Secondary findings include medically important genes recommended by the ACMG (PMIDs: 25356965, 27854360).
Incidental findings will be limited to pre-symptomatic status for a late-onset disorder (e.g. deletion in tumor suppressor genes).

Probable carrier status: focal deletion of a gene that causes an autosomal recessive disorder, where loss of function is a mechanism of pathogenicity. May also include recurrent deletions that are known to only confer a phenotype in the homozygous state (e.g. STRC/CATSPER, HBA1/HBA2, etc).
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.

Amniotic fluid, chorionic villus sampling (CVS) or products of conception specimen can be used for additional testing if sufficient specimen is received by the laboratory. Please contact the laboratory for more information.
Additional Tests Performed: 

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