Detection of=1?Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Prenatal Diagnosis (Impact Factor: 3.27). 01/2012; 32(1):10-20. DOI: 10.1002/pd.2855
Source: PubMed


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 ~1Mb ina single cell.
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.
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 1.2Mb Williams syndrome deletion, and a 1.3Mb CMT1A duplication. Replicate analyses yielded consistent results.
Aneuploidy and genomic imbalances with CNVs as small as 1.2Mb 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.

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Available from: Sau Wai Cheung,
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    • "Standard DNA-microarrays can detect copy number variations (CNVs) larger than 2.5 Mb from a single-cell genome [20]–[22], while targeted array comparative genomic hybridizations can discover approximately 1 Mb-sized DNA imbalances [23], although remarkably, CNVs as small as 56 kb in single-cell PCR-based WGA products have been detected [24]. Similarly, SNP-arrays can find copy number aberrations encompassing millions of bases in a cell [25]–[28], but have the advantage of enabling the discovery of copy neutral DNA anomalies and regions of loss-of-heterozygosity (LOH), and allow inferring genome-wide haplotypes [29]–[31]. "
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