EpiPsychosis_IGF2

This repo contains code used to generate results for the manuscript:

Differential DNA methylation of an enhancer at the IGF2 locus affects dopamine synthesis in patients with major psychosis*. Pai S., Li P., Killinger B., Marshall L., Jia P., Liao J., Petronis A., Szabó P.E., and Labrie V.

bioRXiv preprint: https://doi.org/10.1101/296756

Prerequisites

Most of the analysis uses R and BioConductor packages. In addition, the standalone packages dataExplore (http://github.com/shraddhapai/dataExplore) and IlluminaEPICtools (contained in IlluminaEPICTools in this repo) are required to be installed.

Case-Control EPIC microarrays

Location: CaseControlEpic/ folder

General

• Array preprocessing QC, normalization, MDS: processInput.R
• Post-processing QC and data exploration, data cleaning, merging with processed genetic data: RunMe.R (Supplementary Figure 3,4)
• Call differentially-methylated probes and plotting results:
  • Main result reported in paper (all samples): callDMPs.R (Supplementary Figure 6a, Supplementary Table 2)
  • CEU samples: callDMPs_CEU.R (Supplementary Table 3)
  • comb-p: combp_new.R
  • IGF2 confirmation with CEU males: dmp_getMeanBetaDiff_CEUmale.R
• Volcano plot in Figure 1A: volcanoPlot.R
• Pathway analysis and Figure 1B: Call to dmp_pathwayORA within callDMPs.R; Enrichment Map created in Cytoscape.
• Compare genotypes with genetic data: Supplementary Fiure 5a: getEPICsnpgeno.R and match_genoEPIC.R

Methylation at IGF2 locus

• Figure 2a: targetView.R
• Figure 2b: dmp_plotGroupMeans.R
• Supplementary Figure 8: Case/control IGF2 methylation plotted with lifestyle variables: relateIGF2_confounds.R

meQTL analysis

• Pre-imputation processing: preimpute_check.sh, vcf4impute.sh
• Extracts genotypes in DMP window: CaseControlSNP/prepareDMPwins.R, CaseControlSNP/getSNPsInRanges.sh
• meQTL analysis: Supplementary Tables 7,8 meQTL_useLMER.R
• meQTL genotype x disease interaction in IGF2 region: Supplementary Table 9: meQTL_IGF2TH_probes.R
• Figure 1c: meQTL_plotCis.R

Case-Control genotyping

Code in CaseControlSNP/

• Quality control: fixPlink_coords.R, plinkQC.sh
• Compute lambda: computeLambda.R

Case-Control targeted bisulfite sequencing

Code in SeqCap1/ and SeqCap2/ Processing pipeline followed manufacturer's instructions from this online document: http://netdocs.roche.com/DDM/Effective/07187009001_RNG_SeqCap-EZ_TchNote_Eval-data_v2.1.pdf

• Processing:
  • QC of fastq files: fastQC_batch.R
  • Trim reads: trim.sh
  • Count reads: countreads.sh
  • Align reads: align.sh
  • Post-alignment processing: postalign_runner.sh > postalign.sh
• Validation of IGF2 locus: Figure 2c,d: IGF2_view.R
• Correlate IGF2 methylation with EPIC microarrays: Supplementary Figure 9: corrEPIC_IGF2.R

Case-Control transcriptomes

Code in CaseControlRNA/

• Processing: SCZ_RNAseq.bash
• Differential expression and pathway analysis: diffEx_simple.R (Supplementary Table 5,6). Enrichment Map created in Cytoscape.
• Volcano plot:Supplementary Figure 7a: volcanoPlot.R
• Correlation of expression with BrainSpan gene sets: Supplementary Figure 7b: diffEx_annotate.R
• Comparing genotype with SNP arrays: RNAseq_callVar.sh, makePlink.sh, matchGeno.R

Mouse transcriptomes

Code in MouseRNA/

• Processing: ../CaseControlRNA/SCZ_RNAseq.bash
• Differential expression: Figure 4a, Supplementary Figure 14, Supplementary Tables 12,13. diffEx.R
• Pathway analysis: Figure 4b, Supplementary Figure 15, Supplementary Tables 14,15. runPathway_FC.R and runPathway_STR.R. Enrichment map created in Cytoscape.

Mouse Synaptosomes

• Pathway analysis: Supplementary Figure 17, Supplementary Table 19. diffEx_testAllProt.R