Illumina Prenatal Microarray Analysis- Comprehensive (PREC)

Illumina Prenatal Microarray Analysis- Comprehensive (PREC)
WSLH Department: Cytogenetics
WSLH Test Code:890PREC
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 7-10 days, depending on specimen size and condition. Smaller specimens may require additional culture time. (Reports are issued Monday-Friday 7:45 AM - 4:30 PM)
Recommended Uses:Prenatal** The American College of Obstetricians and Gynecologists and the Society for Maternal-Fetal Medicine recommend the use of chromosomal microarray analysis "in patients with a fetus with one or more major structural abnormalities identified on ultrasonographic examination and who are undergoing invasive prenatal diagnosis" and "in cases of intrauterine fetal demise or stillbirth when further cytogenetic analysis is desired". Neonatal** (less than 30 days of age or infants requiring intensive care)- SNP Array Comparative Genomic Hybridization is used to detect large regions of homozygosity as well as gains and losses of DNA from specimens containing high quality genomic DNA. The American College of Medical Genetics and Genomics (ACMG) has recommended that array comparative genomic hybridization (aCGH) 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:** Amniotic fluid (AF): 15-25 ml (discard the first 1-2ml of amniotic fluid to minimize the possibility of maternal cell contamination). **Chorionic villus (CVS): 10-30 mg tissue. ** Products of conception (POC) fresh tissue: placental villus is the preferred tissue; kidney, lung, and/or fascia are also acceptable. Sample size at least 0.3 cm cubed. ** FFPE tissue or frozen tissue: The cytogenetics laboratory will attempt to work with the specimen received and will return any unused material. ** Cultured cells: 3-T25 flasks, 70% confluent. ** In addition, 4ml blood in Sodium Heparin from both parents when available to expedite the interpretation of abnormal findings. **Neonatal: Blood, 2 ml in Sodium Heparin is recommended
Collection Kit/Container: 
Patient Preparation: 
Collection Instructions:** AF: 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 15-30 ml of the remaining amniotic fluid into two or three sterile 15 ml centrifuge tubes. ** CVS: Using aseptic technique, obtain at least 10mg of chorionic villi, taken between 11-38 weeks of gestation. Place villi into a flask with transport media provided by the department. ** POC: 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. **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.
Specimen Handling and Transport:Store and transport specimens at room temperature (may transport with coolant during hot, >85 degrees F weather). DO NOT FREEZE. The laboratory must receive specimens within 24-48 hours of collection.
Unacceptable Conditions:Prenatal specimens: A specimen with no fetal material identified and only maternal decidua present will be rejected. Blood: Blood that is clotted or hemolyzed is not acceptable. Blood must not be frozen. Plasma and serum are not acceptable.
Requisition Form:Cytogenetics Lab Prenatal Diagnosis Form #133
Required Information:Laboratory regulations require the following minimum information to be provided on the requisition form for a specimen to be accepted for testing: Patient name or unique identifier; date and time of collection, patient date of birth and sex, specimen type/site of collection, test request(s), reason for referral, clinician name and UPIN/NPI, and address for reporting results. Please be certain that name/identifier on the form matches that on the specimen label.
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:Standard (may be done as part of a tiered approach) or abridged chromosome analysis (done when a standard chromosome analysis is not performed and when viable tissue is available) (AF- test #850 or #852; CVS- test #855 or #857; POC- test #831)
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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