Cytogenomic Microarray

Clinical Information

The cytogenomic microarray can be utilized as a first-tier test for individuals with autism spectrum disorders, intellectual disability, and multiple congenital anomalies.

Technical Information

Isolated DNA is analyzed using the Illumina Diversity Array + cytogenetic (GDA+Cyto) Microarray system. This diagnostic assay identifies genomic copy number variations and loss of heterozygosity regions. VIA software (BioNano Genomics) is utilized in data analysis. SNP genotyping on this platform has the enhanced ability to identify long contiguous stretches of homozygosity (LCSH) and uniparental disomy; however, this assay cannot detect polyploidy, balanced rearrangements, point mutations, and most mosaic conditions. All copy number changes are determined using the human genome build 38 (hg38/GRCh38).

Copy number variants are reported according to the most recent International System for Human Cytogenetic Nomenclature (ISCN) guidelines. CNV classification is based on the guidelines recommended by the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resources (ClinGen). Reportable variants include pathogenic variants, likely pathogenic variants, and variants of uncertain significance. Likely benign and benign variants are not routinely reported.

Specimen Requirements

• The preferred sample type is 3-4ml of peripheral blood collected in an EDTA (lavender top) tube.  Extracted DNA, saliva, and solid tissue are also accepted for this test. Blood and saliva kits are available by request.
• Send approximately 5µg of extracted DNA at a requested concentration of 90-130 ng/µl.
• Saliva samples must be submitted in an approved saliva kit.
• If sending solid tissue, use a sterile technique to obtain a 5mm biopsy of unmacerated tissue and place in a tube containing transport media or a sterile solution such as a balanced salt solution. For fetal tissue, placental tissue (fetal membranes or chorionic villi) or a piece of amnion is requested in addition to the fetal specimen (for all cases). If fetal samples are obtained at autopsy, skin, gonad or thymus are preferred for chromosome analysis. DO NOT allow the specimen to come into contact with formalin or other fixatives if chromosome analysis is ordered as fixed tissue will not grow for chromosome analysis. Chromosome analysis cannot be performed on FFPE samples.

Transport Instructions

• Blood specimen should be kept at room temperature and delivered via overnight shipping. If shipment is delayed by one or two days, the specimen should be refrigerated and shipped at room temperature. Do not freeze the specimen. Samples collected on Friday can be safely designated for Monday delivery.
• Extracted DNA should be sent at room temperature via overnight delivery.
• Saliva is stable at room temperature and can be delivered via overnight or ground shipping.
• Solid tissue should be kept at room temperature if transported immediately. If the specimen is not being immediately transported to the laboratory, it may be refrigerated. Do not freeze. The sample should be sent by courier or overnight mail to arrive at the laboratory within 24 hours.

Prenatal Testing Information

See prenatal microarray