|Illumina Microarray Analysis- Targeted Family|
| WSLH Department:|| Cytogenetics|
|WSLH Test Code:||890FAM|
|Price:||For pricing information, please call 608-262-0402.|
|Includes:||Previously characterized familial CNVs and regions of homozygosity (ROH). This test may also be used to confirm CNVs or ROH identified in a research laboratory or with another methodology.|
|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:||Approximately 12-21 days, with an average of 12 days. (Reports are issued Monday-Friday)|
|Recommended Uses:||Clinical indications for microarray analysis include congenital abnormalities, developmental delay, autism spectrum disorders, and tumor characterization.|
|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.
|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/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.
|Specimen Handling and Transport:||Store and transport specimens at room temperature (may transport with coolant during hot weather, >85 degrees F). Specimens must be received by the laboratory 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:||Please reference proband's laboratory case number on the requisition form|
|Results include:||Previously characterized familial CNVs and regions of homozygosity (ROH) are reported. This test may also be used to confirm CNVs or ROH identified in a research laboratory or with another methodology.|
|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.|
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