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Whole genome amplification (WGA) artifacts due to uneven replication can create confounding karyotyping results and gaps in copy number analysis. An improved WGA pipeline was tested on a resected glioblastoma tumor and identified additional somatic mosaicism. By initially isolating single cells using CellRaft arrays for NeuN-single nuclei isolation pre-WGA as opposed to bulk DNA sequencing, low-abundance clones with copy number variants in clinically relevant loci not previously identified were found. This improved technique for molecular karyotyping using CellRaft arrays for single-cell nuclei isolation can be used to parse out additional copy number variation and improve full genomic coverage.