Illumina Microarray Analysis
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| WSLH Department: | Cytogenetics |
| WSLH Test Code: | 890 |
| Day(s) Performed: | 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: | |
| Additional Tests Performed: |
| Patient Preparations: | |
| Specimen Requirements: | Blood (including cord blood): 4-6 ml Sodium Heparin Saliva: Isohelix Saliva Collection kit used according to manufacturer instructions Buccal: Stabilized buccal swabs collected with SafeCollect kit (Zymo) according to manufacturer instructions. Skin biopsy: 1-2mm punch biopsy 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 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: | 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. |
| Collection Kit/Container: |
Buccal: SafeCollect collection kit (Zymo)
Prenatal specimens: Cytogenetics and Molecular Genetics Collection Kit Saliva: Isohelix Saliva Collection kit |
| Collection Instructions: | Contact the laboratory (608-262-0402) to obtain desired collection kit. 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/Buccal: 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. 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: | 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 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). For postnatal specimens, CNVs of uncertain clinical significance will be reported when at least one protein coding gene is involved in a copy number loss greater than 200 kilobases (kb) or a copy number gain greater than 500 kb. Smaller CNVs (less than 200-500 kb) 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. For prenatal specimens (including products of conception), CNVs of uncertain clinical significance will be reported when at least one protein coding gene is involved in a copy number loss greater than 1 Megabase (Mb) or a copy number gain greater than 2 Mb. Smaller CNVs (less than 1-2 Mb) 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. Likely benign and benign CNVs are not reported. 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). Whole genome 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. |
| 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 losses greater than 20-kilobases (kb) in size and copy number gains greater than 50-kb in size (smaller changes may be detected depending on gene content and probe number). The assay is validated to detect copy neutral loss of heterozygosity greater than 3-Mb in size (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 long-range PCR, 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. |
| Methodology: | Isolated genomic DNA is quantified, amplified, fragmented, and hybridized to the Illumina Global Diversity Array with Cytogenetics-8 (GDACyto) bead chip that contains 1.8 million different locus-specific 50-mer probes with at least 15x redundancies. The 1.8 million probes have an average probe spacing of 20-kilobases (kb) across the whole genome (backbone coverage) and increased probe spacing (5-kb) in targeted clinically relevant genes. Fluorescence type and intensity of each probe is compared to a custom cluster file using Illumina's Beeline or iScan control software. Data analysis is performed using Genome Studio and Bionano's VIA 7.0 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), gnomAD (https://gnomad.broadinstitute.org/) and DECIPHER (https://decipher.sanger.ac.uk/). Normal limits have been determined by UWCMGS 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. |
| Includes: | High resolution, genome-wide assessment of copy number variants (CNVs) and absence of heterozygosity (AOH). |
| CPT Code: | 81229 |
| Price: | For pricing information, please call 608-262-0402. |