ORIGINAL ARTICLE Detection of ≥1 Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays Weimin Bi 1 , Amy Breman 1 , Chad A. Shaw 1 , Pawel Stankiewicz 1 , Tomasz Gambin 1,2 , Xinyan Lu 1 , Sau Wai Cheung 1 , Laird G. Jackson 3 , James R. Lupski 1 , Ignatia B. Van den Veyver 1,4 and Arthur L. Beaudet 1 * 1 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA 2 Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland 3 Department of Obstetrics and Gynecology, Drexel University College of Medicine, Philadelphia, PA, USA 4 Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA *Correspondence to: Arthur L. Beaudet. E-mail: abeaudet@bcm.tmc.edu ABSTRACT Objective High resolution detection of genomic copy number abnormalities in a single cell is relevant to preimplantation genetic diagnosis and potentially to noninvasive prenatal diagnosis. Our objective is to develop a reliable array comparative genomic hybridization (CGH) platform to detect genomic imbalances as small as ~1 Mb in a single cell. Methods We empirically optimized the conditions for oligonucleotide-based array CGH using single cells from multiple lymphoblastoid cell lines with known copy number abnormalities. To improve resolution, we designed custom arrays with high density probes covering clinically relevant genomic regions. Results The detection of megabase-sized copy number variations (CNVs) in a single cell was influenced by the number of probes clustered in the interrogated region. Using our custom array, we reproducibly detected multiple chromosome abnormalities including trisomy 21, a 1.2 Mb Williams syndrome deletion, and a 1.3 Mb CMT1A duplication. Replicate analyses yielded consistent results. Conclusion Aneuploidy and genomic imbalances with CNVs as small as 1.2 Mb in a single cell are detectable by array CGH using arrays with high-density coverage in the targeted regions. This approach has the potential to be applied for preimplantation genetic diagnosis to detect aneuploidy and common microdeletion/duplication syndromes and for noninvasive prenatal diagnosis if single fetal cells can be isolated. © 2012 John Wiley & Sons, Ltd. Funding sources: None Conflicts of interest: None declared Supporting information may be found in the online version of this article. INTRODUCTION Single-cell array comparative genomic hybridization (CGH) provides information on genome copy number changes at the single cell level, which is of great importance in both cancer genetics and clinical diagnosis. This single cell technology facilitates the studies of tumor heterogeneity, micrometastases, and minimal residual disease. In addition, the application in preimplantation diagnosis allows a comprehensive chromosome analysis including aneuploidy analysis of all 24 chromosomes. Furthermore, single-cell analysis may open up new opportunities for noninvasive prenatal genetic diagnosis. It has been well documented that fetal cells, cell-free fetal (cff) DNA, and RNA are present in the peripheral blood circulation of pregnant women. 1 In addition, fetal trophoblasts have been identified in endocervical specimens at an early stage of gestation. 2,3 Cell-free fetal DNA is relatively abundant in the maternal circulation but it is fragmented and not physically separated from cell-free maternal DNA. In contrast, the genomic DNA of circulating intact fetal cells represents a complete fetal genome that is physically separated from maternal cellular and cell-free DNA. Although circulating fetal cells are very rare, at about one cell per ml of maternal blood, 4 their genetic information is accessible by single cell technologies, 5 such as whole- genome amplification (WGA), which can generate sufficient DNA for array CGH. Prenatal Diagnosis 2012, 32, 10–20 © 2012 John Wiley & Sons, Ltd. DOI: 10.1002/pd.2855