DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder (Methylation)

We fine-mapped DNA methylation in neuronal nuclei (NeuN+) isolated by flow cytometry from post-mortem frontal cortex of the brain of individuals diagnosed with schizophrenia, bipolar disorder, and controls (n=29, 26, and 28 individuals). Whole-genome DNA methylation profiling for each sample was done with Illumina MethylationEPIC BeadChip microarrays at the The Centre for Applied Genomics (Toronto, Canada). Bisulfite converted DNA samples (n=104) were randomized across arrays (8 samples/array). Data generated from the microarrays were preprocessed with Minfi v1.19.12. Normalization was performed with noob, followed by quantile normalization. All samples had sex matching that predicted from the methylome. Probes that overlapped SNPs (MAF > 5%) on the CpG or single-base extension were excluded (11,812 probes), as were probes known to be cross-reactive (42,558 probes; PMID: 27330998) and those that failed detectability (P>0.01) in >20% samples (1,170 probes). After processing, 812,663 probes were left. Based on principal component analysis (PCA) co-clustering, one sample, despite being labeled NeuN+, clustered with NeuN- samples and was excluded from downstream analyses. Surrogate variable analysis identified no such variables; for this the null model used age and sex as covariates, while the full model included diagnosis.