UF Cytogenetic Laboratory Microarray Analytic Methodology to Combine SNP with CGH Analyses into a Single Test

Internal validation of the International Standards for Cytogenomic Arrays-endorsed SurePrint G3 Human CGH+SNP© microarray has been completed by our Cytogenetics Laboratory and is now available as part of our Test Directory

The SurePrint G3 Human CGH+SNP© microarray design combines single nucleotide polymorphism analyses (SNPs) with oligonucleotide comparative genomic hybridization analyses and is based on the recommendations of the International Cytogenetic Array Consortium for standards, resolution and content, using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. It was designed to detect genomic-wide absences of heterozygosity (AOH) because of apparent common descent, uniparental isodisomy and some forms of segmental AOHs, in addition to the detection of copy number variants (CNVs) as DNA gains or losses across the genome.

Note: This array format will replace the previous ISCA 180k format as the default testing modality utilized for all new and pending congenital aCGH testing requests. The 180k and 44k oligonucleotide formats may be employed for direct comparison purposes for additional family members previously studied by these designs, where necessary. Contact the Laboratory before ordering to request for testing to be performed by an alternate design or platform.

Resolution and Method Performance Specifications:The SurePrint G3 Human CGH+SNP© was built using a commercial platform (Agilent Technologies), and it contains ~120k oligonucleotide features (~60mers) that represent coding and non-coding human sequence in the genome and ~60k SNP features (content sourced from the UCSC GRCh37/hg19 human genome; Feb. 2009).

This array contains high-density, genome-wide coverage of clinically relevant deletion/duplication syndromes and the subtelomeric and pericentromeric regions with an average probe spacing of ~25kb. It is designed to detect gains and losses at a minimum of ~500 kb across the genome or smaller when occurring within the ~500 targeted regions of known microdeletion/duplication syndromes or gene-rich areas. Resolution for segmental AOHs is limited to contiguous stretches of 5 mb or greater but may be reported for smaller sizes when detected in regions currently known or implicated in imprinting conditions associated with AOH. 

Turnaround time averages about three to four weeks. Confirmatory testing for abnormal findings will delay final reporting.

If you have questions on the availability or applications of specific microarray platforms, call the Cytogenetics Laboratory at:

(352) 265-9900

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