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For identifying potential aneuploidy in normal somatic tissues, techniques such as fluorescence in situ hybridization (FISH) and single-cell low-coverage whole genome sequencing (scL-WGS) have been utilized. The accuracy of these techniques including prevalence for false positive/negative accounts of aneuploidy have been inconsistent. To understand the efficiency of these techniques, cells with naturally occurring or induced aneuploidy were generated and isolated with the CellRaft single cell picking system. After CellRaft isolation, these single cells were amplified and sequenced with scL-WGS. The results showed that scL-WGS frequently underestimated aneuploidy levels while FISH overestimated, and a modified 2-probe approach can be used as additional detection for low levels of aneuploidy.