This study characterized somatic mutations in chronic traumatic encephalopathy (CTE) and performed whole-genome sequencing of single neurons isolated from prefrontal cortex (PFC) of postmortem human brain of individuals with CTE, repetitive head impacts but without CTE (RHI), 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 primary template-directed amplification (PTA) or multiplexed end-tagging amplification of complementary strands (META-CS).