Comparison of three whole genome amplification methods for detection of genomic aberrations in single cells

Objective Detection of genomic copy number abnormalities in a single cell using array comparative genomic hybridization (CGH) offers a promising non‐invasive alternative for prenatal diagnosis. Our objective was to compare three commercially available whole‐genome amplification (WGA) kits for their capacity to produce high quality DNA from single cells that is suitable for both molecular genotyping and array CGH. Methods We examined kit performance on unfixed, fixed and fixed/permeabilized lymphoblastoid cells. Molecular genotyping methods were used to evaluate the fidelity of amplified DNA for genomic profiling, while array CGH was used to assess copy number from single cells harboring trisomy 21, a DiGeorge syndrome deletion, a CMT1A duplication or a MECP2 duplication. Results Molecular genotyping was achieved from single cells but performance varied between WGA kits. Furthermore, we consistently detected a dosage difference in sex chromosomes for gender mismatched hybridizations and for chromosome 21 in trisomy 21 cells. The 2.5 Mb DiGeorge syndrome deletion was also detected using all three WGA platforms, whereas the 1.3 Mb CMT1A and the 0.6 Mb MECP2 duplications were not consistently detected. Conclusion These data suggest that single cell molecular genotyping and copy number analysis can be accomplished when WGA conditions are optimized. © 2016 John Wiley & Sons, Ltd. What's Already Known About This Topic? Genome‐wide copy number analysis of single cells has been applied to whole‐genome amplification (WGA) products by both array comparative genomic hybridization (CGH) and next‐generation sequencing. We have previously shown that array CGH using single cell WGA DNA could detect copy number changes larger than 1 Mb using a custom array. What Does This Study Add? This study demonstrates successful array CGH analysis on both fixed and unfixed single cells, and compares WGA kit performance for each condition. We show that molecular genotyping can be reliably performed on fixed and unfixed single cells but performance varies between WGA kits. These analysis methods have the potential to be used for cell‐based non‐invasive prenatal copy number analysis.