We modeled differences in diagnosis, controlling for age, sex, race, and the first 4 PCs from the negative control probes ultimately among 108 patients with schizophrenia and 136 controls. Sex was not associated with diagnosis, and therefore not included as an adjustment variable (p=0.16, see Supplementary Table 1). Smoking status was obtained by toxicology, where those positive for smoking tested positive for either nicotine and/or cotinine, and included in the above model to assess confounding by smoking. Similarly, cell composition estimates were included in the above model to assess potential confounding by composition differences between cases and controls. We performed a Chi-squared test (df=1) to determine whether CpGs showing diagnostic effects were over- or under-enriched for meQTLs.
