Validation and implementation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance

Abstract

BackgroundSeveral studies have demonstrated that array comparative genomic hybridisation (CGH) for genome-wide imbalance provides a substantial increase in diagnostic yield for patients traditionally referred for karyotyping by G-banded chromosome analysis. The purpose of this study was to demonstrate the feasibility of and strategies for, the use of array CGH in place of karyotyping for genome imbalance, and to report on the results of the implementation of this approach.ResultsFollowing a validation period, an oligoarray platform was chosen. In order to minimise costs and increase efficiency, a patient/patient hybridisation strategy was used, and analysis criteria were set to optimise detection of pathogenic imbalance. A customised database application with direct links to a number of online resources was developed to allow efficient management and tracking of patient samples and facilitate interpretation of results. Following introduction into our routine diagnostic service for patients with suspected genome imbalance, array CGH as a follow-on test for patients with normal karyotypes (n = 1245) and as a first-line test (n = 1169) gave imbalance detection rates of 26% and 22% respectively (excluding common, benign variants). At least 89% of the abnormalities detected by first line testing would not have been detected by standard karyotype analysis. The average reporting time for first-line tests was 25 days from receipt of sample.ConclusionsArray CGH can be used in a diagnostic service setting in place of G-banded chromosome analysis, providing a more comprehensive and objective test for patients with suspected genome imbalance. The increase in consumable costs can be minimised by employing appropriate hybridisation strategies; the use of robotics and a customised database application to process multiple samples reduces staffing costs and streamlines analysis, interpretation and reporting of results. Array CGH provides a substantially higher diagnostic yield than G-banded chromosome analysis, thereby alleviating the burden of further clinical investigations.

Safety paradigm: genetic evaluation of therapeutic grade human embryonic stem cells

“…This rapid replacement of karyotype analysis by array CGH testing is fuelled by the greatly increased resolution of array CGH, and the objectivity and ease of the analytical process. Various different array CGH platforms are commercially available; most diagnostic laboratories are in agreement that platforms comprising oligonucleotide probes have better resolution and provide more accurate and reproducible results than those comprising bacterial artificial chromosome clones ( Ylstra et al 2006;Ahn et al 2010). Oligonucleotide array platforms are available in a number of formats, with different probe densities across the genome.…”

“…In addition, in shorter chromosome preparations, such as those typically obtained from cell lines, only abnormalities of whole chromosome copy number and very large imbalances can confidently be assigned (figure 3). Advances in molecular cytogenetic technologies have recently led to the introduction of array comparative genomic hybridization (CGH) as either an add-on test following karyotype analysis for the detection of chromosome imbalance (Edelmann & Hirschhorn 2009) or, in an increasing number of centres, as a first-line test (Ahn et al 2010). This rapid replacement of karyotype analysis by array CGH testing is fuelled by the greatly increased resolution of array CGH, and the objectivity and ease of the analytical process.…”

“…There are currently no standardized overall costs for either karyotype analysis or array CGH testing; these costs are highly dependent on local conditions at testing laboratories. However, by using parsimonious hybridization strategies, robotics and batch testing, some laboratories are already able to offer array CGH testing at the same price as karyotype analysis (Ahn et al 2010). Sending stem cell samples to an existing centre that carries out routine array CGH analysis is therefore a cost-effective and efficient way of collecting the information necessary for proper characterization of genetic imbalance in these cell lines.…”

Array-CGH analysis in patients with intellectual disability and/or congenital malformations in Brazil

“…In addition, microarray analyses provide accurate diagnosis in approximately twice as many cases as classical karyotyping and fluorescent in situ hybridization (Gijsbers et al, 2009;Hochstenbach et al, 2009;Ahn et al, 2010;Miller et al, 2010). In recent years, approximately 15-20% of ID cases are caused by submicroscopic CNVs (Zahir and Friedman, 2007;Gijsbers et al, 2009).…”

Comparison of Two Microarray CGH Platforms for Genome-Wide Copy Number Profilings: Oligo-Based Arrays Versus Bacterial Artificial Chromosome Arrays

“…Data from the study of Ou et al clearly showed that oligo-based arrays offered a valid alternative for focused BAc arrays, furthermore without the need for dye-swap experiment (10). in another study 42 patients were tested on both BAc and oligo array platforms where discordance was found in six cases -BAc arrays failed to detect the imbalances (1). the genome-wide analysis for CNVs in a set of 19 patient probes BAC platforms identified 71 deletions and 74 amplifications, whereas the oligo platform detected 314 deletions and 209 amplifications with median lengths of 12 Mbp and 3.5 Mbp respectively (22).…”