Refinement of Schizophrenia GWAS Loci using Methylome-wide Association Data: Supplementary Material

Gaurav Kumara , Shaunna L. Clarka, Joseph L. McClaya, Andrey A. Shabalina, Daniel E. Adkinsa, Linying Xiea, Robin Chana, Srilaxmi Nerellaa, Yunjung Kimc, Patrick F. Sullivanc,b , Christina M. Hultman b, Patrik K.E. Magnusson b, Karolina A. Aberga and Edwin JCG van den Oord*,a

a Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond ,VA, USA

b Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden

c Department of Genetics, University of North Carolina at Chapel Hill, NC, USA

*Corresponding author:

Dr. Edwin JCG van den Oord.

Center for Biomarker Research and Personalized Medicine,

School of Pharmacy, McGuire Hall, Room 209.

P. O. Box 980533. Richmond, VA 23298-0581

E-mail:

Phone: +1 (804) 628-7614

Fax: +1 (804) 628-3991.

Table S1. Design features of pyrosequencing assays

Location / Primers
Chr Begin End Strand / Forward PCR / Reverse PCR / Sequencing
SDCCAG8 / 1 / 243493888 / 243493966 / + / GGTAGGTTTTAATTTAGTGTGATTAGTTG / Biot-CCCTTTTCTCTTACTAAAATACAAATTCT / GGAGTTGGAGAGGTA
CREB1 / 2 / 208461648 / 208461657 / + / AAGGTAATTTAAAATAAATATGTGGAAAT / Bio-ACTTTTAACTCCTCAATCAATATCTTAT / GTTTGTAGGGAAGTAGTT
ATXN7 / 3 / 63980718 / 63980830 / - / GGATTGTTAATTATTAAATTTTTTGTAGAG / Biot-CCCTTCCTTTTCTCTCATTCAT / GTAGAGAGAGTTATTTTTAGTTTAA

Note: The locations are given for the CpGs targeted in each assay. Strand indicates if the assays were designed on the upper (+) or the lower (-) strand. The three primers used for each assay are given. The direction of the sequencing primer is always the opposite of the biotinylated primer.

Chr / MWAS start coordinate / MWAS end coordinate / Gene name / tfbsConsSites (start_coord – end_coord)
1 / 243493888 / 243493966 / SDCCAG8 / http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$MYOGNF1_01(243493836--243493865)
2 / 149876935 / 149877120 / KIF5C/LYPD6B / http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$FREAC4_01(149877087--149877103)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$ER_Q6(149877311--149877330)
2 / 208461619 / 208461657 / CREB1/METTL21A / http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$EVI1_04(208461678--208461693)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$IRF1_01(208461710--208461723)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$FOXO1_02(208461713--208461727)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$SRY_02(208461716--208461728)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$PBX1_01(208461728--208461737)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$NKX22_01(208461744--208461754)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$NKX25_01(208461747--208461754)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$NFAT_Q6(208461808--208461820)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$YY1_01(208461809--208461826)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$CP2_01(208461822--208461833)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$E2F_02(208461888--208461896)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$EN1_01(208461907--208461914)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$MEIS1AHOXA9_01(208461938--208461952)
3 / 63980718 / 63980830 / ATXN7/LOC100507062/PSMD6 / http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName= V$NFKB_C(63981178--63981190)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName= V$CREL_01(63981179--63981189)
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=V$NFKAPPAB_01(63981179--63981189)

Table S2. MWAS (CpG) blocks (+/- 250bp) associated with transcription factor binding conserved sites (tfbsConsSites).

Figure S1. Power to detect methylation sites that tag allele frequency differences between cases and controls.

Note: The y-axis shows the log 10 of the sample size required to detect SNPs that are meQTLs with 80% power while controlling the FDR at the 0.1 level. The effect size of the meQTL is indicated on the x-axis in terms of the proportion of variance of the total variation (=0.01, 0.03, and 0.05) in methylation it explains, The odds ratios indicate the allele frequency difference between cases and controls where ratios of 1.2 and 1.5 indicate a risk allele and ratios of 0.83 (=1/1.2) and 0.67 (=1/1.5) a protective allele. For each odds ratio there are three points in the figure that correspond with minor allele frequencies in controls of 0.05, 0.2, and 0.5. FDR control depends on the proportion of tests for which the null hypothesis is true. This proportion was assumed to be 0.999.