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In the brain, it is recognized that the presence of somatic mutations and copy number variants exist. This study focused on comparing different amplification methods for single-cell whole genome amplification prior to sequencing. Tissue was prepared and 5,000 nuclei were diluted to be dropwise seeded onto a CellRaft Array. Using a reliably established protocol for nuclei extracting using the CellRaft Array, CellRafts containing single nuclei with neuronal appearance were isolated and deposited into tubes for amplification. To avoid cross contamination among nuclei, the magnetic collection wand was rinsed sequentially with DNase-I solution. Three methods of scWGA were compared: PicoPLEX, PTA, and dMDA before being sequenced and analyzed.