This study performed whole-genome sequencing of single neurons isolated from prefrontal cortex (PFC) and hippocampus CA1 (HC) of postmortem human brain of individuals with Alzheimer’s disease (AD)(Braak stage V-VI) or non-disease control, along with bulk whole-genome sequencing performed on each individual as a reference genome for variant calling. Single neuron genomes were amplified using multiple-displacement amplification (MDA) or primary template-directed amplification (PTA).