Comparison of Targeted and Whole Genome Analysis of Postnatal Specimens Using a Commercially Available aCGH Microarray Platform

Abstract

Purpose: The University of Utah Comparative Genomic Hybridization Microarray Laboratory was one of the first U.S. laboratories to offer comparative genomic hybridization microarray testing using a commercial platform in a clinical setting. Results for 1075 patients (1596 chips) are presented.

Methods: The Spectral Genomics/PerkinElmer Constitutional Chip TM (targeted array), SpectralChip 2600 TM (whole genome array) and a "Combo" chip (both arrays run simultaneously) were the tests offered. Abnormal results were confirmed by an alternative method, most often fluorescence in situ hybridization.

Results: In 669 cases with known normal cytogenetics, an abnormal detection rate of 10.8% was observed, (5.3%, 12.2% and 14.1% for the Constitutional Chip TM, SpectralChip 2600 TM and Combo assay, respectively). Known copy number variants and single clone abnormalities are not included in these rates. Single clone abnormalities are reported separately. For 1075 total cases, we report an average abnormal rate of 16.8% (8.1%, 23.7% and 18.4% for the three assays). This rate includes characterization of some abnormalities previously identified by cytogenetics.

Conclusions: Comparative genomic hybridization microarray provides a likely etiology for the clinical phenotype in many cytogenetically normal cases, and a whole genome array generally identifies copy number changes more effectively than a targeted chip alone.