CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder.

RNA-seq quality control metrics stratified by disease status. All samples from the 4 brain banks are shown.

Integrated quality control of RNA-seq data. (a) Principal components analysis of log2 CPM values from RNA-seq across 4 brain banks. Brain bank, age of death, and diagnosis are indicated in the legend. (b) Plot of log2 CPM expression of UTY gene from chrY against XIST gene from chrX in order to validate reported sex.

Sex check of ATAC-seq samples. (a) Heterozygosity rate of chromosome X genotype calls outside pseudoautosomal regions. (b) Read counts in OCRs on chromosome Y outside the pseudoautosomal region. (c,d) The read counts of OCRs adjacent to XIST and FIRRE genes.

Quality control metrics for ATAC-seq samples. Histograms of (a) fraction of uniquely mapped reads (mean 0.919, sd ±0.010), (b) fraction of mitochondrial chromosome reads (mean 0.089, sd ±0.022), (c) mean insert sizes of pair-end reads (mean 288, sd ±29), (d) mean GC content (mean 0.418, sd ±0.012), (e) number of called peaks (mean 14,810, sd ±8,979), (f) mean coverage (mean 2.473, sd ±0.642), (g) normalized strand cross-correlation coefficient (mean 1.054, sd ±0.020), (h) relative strand correlation coefficient (mean 0.991, sd ±0.084)) and (i) fraction of fragments in peaks (FRiP) (mean 0.151, sd ±0.027).

Summary of ATAC-seq data. (a) Genomic annotation of consensus OCRs (OCRs within 3 kb of a transcription start site were considered as promoter OCRs). (b) Clustering of the individual samples (n = 269) by chromatin accessibility in consensus OCRs using multidimensional scaling.

Quality control of genotype data. Genotype QC for sex (a,b) and ancestry inference (c,d) for MSSM-Penn-Pitt (a,c) and HBCC (b,d). (a,b) F statistic from plink’s check-sex function, plotted by reported sex. Following data QC there is 100% concordance between reported sex and inferred sex based on F statistic for both MSSM-Penn-Pitt (a) and HBCC (b). (c,d) The first two principal components (PC) of genetic ancestry as inferred by GEMTOOLs. For both MSSM-Penn-Pitt (c) and HBCC (d) we see good concordance between reported ethnicity and genetic background clusters inferred by GEMTOOLs.

Assessing sample concordance using genetic variants. Estimating contamination using Chipmix (x-axis) and Freemix (y-axis) output from VerifyBamID, on RNA-seq and genotyping data for HBCC and MSSM-Penn-Pitt cohorts. Each point is an RNA-seq sample and is colored according to whether the sample was accepted, excluded or rescued. Box in lower left-hand corner indicates criteria for a sample to be accepted if samples match the expected individual. Box in lower right indicates samples that were rescued by re-labeling to the proper individual. We note that this figure included samples there were excluded because of other filters.