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Sensitivity of Comparative Genomic Hybridization Using Artificial Mosaicism and Small DNA Quantities

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Olivier Pichon1, Morgan Mathieu2
1Service de Génétique Médicale, CHU de Nantes, France
2Enzo Life Sciences, Lausen, Switzerland

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INTRODUCTION

Microarray-based comparative genomic hybridization (array CGH) is a fast genome-wide screening tool for the detection with high resolution of a large number of chromosomal anomalies, both constitutional and acquired, in the form of copy number variations (CNVs). This relatively simple technology has been used extensively in clinical settings including prenatal and postnatal diagnostics as well as oncological prognostics.

Despite several studies validating array CGH for the detection of cytogenetic aberrations, only a few have reported on array sensitivity and the ability to detect chromosome imbalances when the DNA is extracted from a heterogeneous cell population containing cells with normal karyotype and cells with unbalanced abnormalities.

The cytogenetics laboratory of the CHU Nantes (France) performs the cytogenetics analyses of prenatal and postnatal samples. Karyotyping, fluorescence in situ hybridization (FISH), and array CGH are techniques used on a regular basis to deliver cytogenetic diagnostics. The issue of array sensitivity is especially relevant for the scientists working on the CGH platform as they have to analyze samples with acquired mosaicism such as tumor biopsies where abnormal cells often coexist with normal cells.

The objective of this study was, therefore, to determine the sensitivity of whole-genome array CGH by creating an artificial mosaicism with low DNA inputs and mixing DNA from a sample with well-characterized genomic anomalies with DNA from a sample with normal karyotype. These DNA pools were then labeled with Enzo’s CYTAG® SuperCGH Labeling Kit before hybridization onto SurePrint G3 human CGH 8x60k microarray. Upon labeling of 50 ng of DNA with CYTAG® SuperCGH Labeling Kit, the lowest limit of detection was deemed to be 10% in the sample examined.

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