Targeted Infertility Microarray

Clinical Information

Y chromosome infertility is characterized by azoospermia or oligospermia and is caused by a hemizygous deletion of Yq involving the AZF (azoospermia factor) regions or a pathogenic variant in USP9Y. There are three defined AZF regions: AZFa, AZFb, and AZFc. This targeted infertility microarray can detect deletions in the AZF regions. Other regions of the genome are not analyzed in the targeted infertility microarray.

Technical Information

Isolated DNA is analyzed using the Illumina Diversity Array + cytogenetic (GDA+Cyto) Microarray system. This diagnostic assay targets genomic copy number variations within the AZFa, AZFb, and AZFc regions on the Y chromosome. 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 (purple top) tube. Additional accepted sample types include extracted DNA or saliva. 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.

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.