SCIENTIFIC DATA | Large eQTL meta-analysis reveals di昀؀ering patterns between cerebral cortical and cerebellar brain regions Solveig K. Sieberts 10 Thanneer M. Perumal 10 Minerva M. Carrasquillo 5 Mariet Allen 5 Joseph S. Reddy 5 Gabriel E. Ho昀؀ man 8 9 Kristen K. Dang 10 John Calley 7 Philip J. Ebert 7 James Eddy 10 Xue Wang 5 Anna K.Greenwood 10 Sara Mostafavi 0 3 6 The CommonMind Consortium (CMC) 1 The AMP-AD Consortium 1 Larsson Omberg 10 Mette A. Peters 10 Benjamin A. Logsdon Lara M. Mangravite 10 .Canadian Institute for Advanced Research, CIFAR Program in Child and Brain Development , Toronto, Ontario , Canada A list of authors and their aoliations appears at the end of the paper Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center , New York, NY, 10032 , USA Centre for Molecular Medicine andTherapeutics , Vancouver, British Columbia , Canada Department of Neurology, Mayo Clinic Florida , Jacksonville, FL, 32224 , USA Department of Neuroscience, Mayo Clinic Florida , Jacksonville, FL, 32224 , USA Departments of Statistics and Medical Genetics, University of British Columbia , Vancouver, British Comlubia , Canada Lilly Research Labs, Eli Lilly and Company , Indianapolis, IN, 46225 , USA Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , NewYork, NY, 10029, U , USA SIAca.hn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , NewYork, NY, 10029 , USA Sage Bionetworks , Seattle, WA, 98121 , USA 2020 7 24 8 2020 28 5 2019

www.nature.com/scientificdata The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer's Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million signi昀؀cant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 signi昀؀cant eQTL for >10,000 genes). We 昀؀nd substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the GenotypeTissue Expression (GTEx) Project eQTL. Additionally, we observed di昀؀erences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).

-

ANALYSIS

Unique Genes

Cis eQTL* with Signif. eQTL eQTL (Genes) not Present in GTEx**

Meta-eQTL (Genes)

not found in Cohort

Genes w/o eQTL in CMC, ROSMAP, HBCC or Mayo TCX Cohort

(typically 100–150). Recently, eforts to understand gene expression changes in neuropsychiatric23–26 and neurodegenerative diseases27–34 have generated brain RNA-seq from disease and normal tissue, as well as genome-wide genotypes. These analyses have found little evidence for widespread disease-specific eQTL, as well ashigh cross-cohort overlap24,35, meaning that most eQTL detected are disease-condition independent. Vis implies that meta-analysis across disease-based cohorts will capture eQTL which are unconfounded by disease state despite diferences in disease ascertainment of the samples,and leverages thousands of available samples to produce a well-powered brain eQTL resource for use in downstream research.

Here we generate a public eQTL resource from cerebral cortical tissue using 1433 samples from 4 cohorts from

the CommonMind Consortium (CMC)23,24,26 and the Accelerating Medicines Partnership for Alzheimer9s Disease (AMP-AD) Consortium30,31, as well as from cerebellum using 261 samples fromAMP-AD. We show that eQTL discovered in GTEx, which consists of control individuals (without disease) only, are replicated in this larger brain eQTL resource. We further show widespread diferences in regulation between cerebral cortex and cerebellum.

To demonstrate one example of the utility of thesedata, we apply a colocalization analysis, which seeks to identify

expression traits whose eQTL association pattern appears to co-occur at the same loci as the clinical trait association, to identify putative genes underlying the GWAS association peaks for schizophreni3a6. Results

We generated eQTL from the publicly available AMP-AD (ROSMAP27,28,35,37, Mayo RNAseq29,38–40) and CMC23,24,26 (MSSM-Penn-Pitt24,26, HBCC26) cohorts with available genotypes and RNA-seq data, using a com

mon analysis pipeline (Supplementary Table 1) (https://www.synapse.org/#!Synapse:syn17015233). Analyses proceeded separately by cohort. Briefy, the RNA-seq data were normalized for gene length and GC content prior to adjustment for clinical confounders, processingbatch information, and hidden confounders using Surogate

Variable Analysis (SVA41). Genes having at least 1 count per million (CPM) in at least 50% of samples were

retained for downstream analysis (Supplementary Table 2). Genotypes were imputed to the Haplotype Reference

Consortium (HRC) reference panel42. eQTL were generated adjusting for diagnosis (AD,control, other for AMP-AD cohorts and schizophrenia, control, other for CMC cohorts) and principal components of ancestry

separately for ROSMAP, Mayo temporal cortex (TCX),Mayo cerebellum (CER), MSSM-Penn-Pitt, and HBCC.

For HBCC, which had a small number of samples derived from infant and adolescents, we excluded sampleswith

age-of-death less than 18, to limit heterogeneity due to diferences between the mature and developing brain.

We then performed a meta-analysis using the eQTL form cortical brain regions from the individual cohorts (dorsolateral prefrontal cortex (DLPFC) from ROSMA,PMSSM-Penn-Pitt, and HBCC and TCX from Mayo). Ve meta-analysis identifes substantially more eQTL than the individual cohorts (Table 1, Fig. 1). Vere is a strong relationship between the sample size in the individual cohorts and meta-analysis and the number of signifcant eQTL and genes with eQTL (Fig. 1b,c). Notably, the meta-analysis identifed signifcant eQTL (at FDR ≤ 0.05) in >1000 genes for which no eQTL were observed in any individual cohort. Additionally, we fnd signifcant eQTL for 18,295 (18,433 when considering markers with minor allele frequency (MAF) down to 1%) of the 19,392 genes included in the analysis.

We then compared our cortical eQTL to those from GTEx (v7)21, which is the most comprehensive brain

eQTL database available in terms of number of availbale brain tissues (Table 1, Table 2). Due to the substantially larger power in these data, we fnd >3.8 million eQTL not identifed in GTEx cortical regions (Anterior Cingulate Cortex, Cortex or Frontal Cortex) and we fnd eQTL for>11,000 genes with no eQTL in these cortical regions in GTEx. While GTEx employs a stricter approach to the control of false discovery rate (FDR)w,e fnd that re-analysis of the GTEx cortical regions usingan approach similar to ours (see Methods) did not account for the number of eQTL and genes with eQTL discoveerd in this analysis, but not in GTEx (3,619,693 and 6,866 for eQTL and genes, respectively, when using the less conservative approach). Next, we evaluated the replication within our cortical and cerebellar eQTL of the region specifc eQTL identifed in GTEx. Ve cortical eQTL generated through the current analyses strongly replicate the eQTL available through GTEx, not only for cortical regions, but for all brain regions including cervical spinal cord (Table 2). Interestingly, the replication in these cortical eQTL of eQTL derived from the two GTEx ceerbellar brain regions (cerebellum and cerebellar hemisphere) is consistently lower than for other brainregions represented in GTEx. However, replication of GTEx cerebellar eQTL is high when compared to the cerebellar eQTL generated in this analysis from the Mayo Clinic

CER samples. We also performed the reverse comparison, by examining the replication of our eQTL in those region-specifc eQTL identifed in GTEx. Unsurprisingly, the replication levels were substantially lower, due to

a 0 0 3 0 de 25 v r sebo 200 ,) lvaue− 150 p (g1o0 100 L − 0 5 the lower power in the GTEx analyses. Replication rates were not substantially changed by using GTEx eQTL discovered using our less conservative approach.

Additionally, we compared our eQTL to a publically available fetal brain eQTL resource43 and found good rep

lication of these eQTL as well (estimated replication rateπ1 = 0.909 for the cortical meta-analysis, andπ1 = 0.861 for cerebellum), though somewhat lower than the replication observed in the GTEx cohorts, which are comprised of adult-derived samples.

Finally, as a proof of concept, we performed a colcoalization analysis between our eQTL meta-analysis and the

Psychiatric Genomics Consortium (PGC) v2 schizophrenia GWAS summary statistics36. Seventeen genes showed posterior probability of colocalization using coloc7 (PP(H4)) > 0.7 (Table 3), with 3 showing PP(H4) > 0.95 (FURIN, ZNF823, RP11-677M14.2). FURIN, having previously identifed as a candidate through colocalization24 has recently been shown to reduce brain-derived neurotrophic factor (BDNF) maturation and secretion when inhibited by miR-338-3p44. ZNF823 has been identifed in previous colocalization analyses45,46. RP11-677M14.2, a lncRNA located inside NRGN, while not previously identifed through colocalization analysis, has been shown to be down-regulated in the amygdala of schizophrenia patients47. Noteably, NRGN does not appear to show eQTL colocalization (PP(H4) = 0.006), instead showing strong evidence for the eQTL and GWAS associations occurring independently (PP(H3) = 0.994). Two additional strong colocalizations THOC7 (PP(H4) = 0.943) and FAM85B (PP(H4) = 0.948) show other potential candidates in the region (Supplementary Table 3). At the THOC7 locus, the competing gene, C3orf49 shows slightly lower strength for colocalization (PP(H4) = 0.820), and the associations do not appear to be independent (R2 between best SNPs = 0.979). At the FAM85B locus, the competing pseudo gene FAM86B3P shows substantially lower evidence for colocalization (PP(H4) = 0.513) and in this case too, the associations appear to be non-independent (R2 = 0.902).

Gene RERE PTPRU FOXN2

C3orf49

THOC7

TBC1D19

CLCN3

PPP1R18 LINC00222 FAM85B

ENDOG

RP11-677M14.2

FURIN CNOT1 ELAC2 ZNF823 PTK6 3

1 1 2 3 4 4 6 6 8 9 11 15 16 17 19 20 eQTL Peak Location* Chr Start 7412645 28563084 47542228 62805378 62819766 25578209 169533866 29644275 108073451 8089567 130581300 123614560 90414642 57553885 11896953 10832190 61160251 End 9877280 30653243 49606348 64834213 64848612 27755954 171644821 31655438 110091064 9084121 132584048 125616016 92426654 59662867 13921426 12840037 62960229

Min(p-value)

NSNPs 4905 4099 5437 4906 4886 4432 4956 1055 3600 3725 3294 5253 4767 5364 5651 3844 4527

GWAS 2.72E-09 1.28E-09 1.66E-06 2.58E-08 2.58E-08 7.44E-07 1.02E-08 1.16E-19 3.37E-08 2.03E-08 1.92E-06 3.68E-12 2.30E-12 1.15E-08 2.84E-06 1.57E-06 4.03E-08 eQTL 2.28E-21 4.42E-10 8.85E-45 1.10E-13 2.21E-39 7.85E-07 1.91E-09 5.52E-07 1.63E-07 5.63E-31 6.90E-62 1.50E-09 1.29E-20 1.16E-06 5.38E-10

Ve replication of fetal eQTL, while signifcant,siosmewhat lower than the replication of adult eQTeLpresented in GTEx. Vis may be due to multiple factors. Ve fetal eQTL analysis was generated frominbrhaomog-e nate, rather than dissected brain regions, thoughhte lower replication likely also refects broad trsacnriptional diferences between developing and mature brain58. Vese transcriptional diferences may also explainwhy we fnd substantially more eQTL than a recently published, similarly sized eQTL analysis which uses samples from across developmental and adult timepoin2t5s, and why this meta-analysis shows higher replicatoin of GTEx eQTL.

Previous studies report a lack of widespread diseea-s pecific eQTL observed in schizophrenia (CMC24) and Alzheimer9s (ROSMAP)35. In accordance, we fnd a strong overlap among eQTacLross disparate disease samples, particularly those with neuropsychiatric nad neurodegenerative disorders, as well as normanldi ividuals from these and other cohorts such as GT24E,3x5. Vis suggests that disease-specifc eQTL, if they xeist, are likely few in number and/or small in efect size, rleative to condition-independent eQTL in general. tIhfey do exist, disease-specifc eQTL discovery may be succes ful in more targeted analyses or with larger samepslizes or meta-analyses, but was not explored for the puorspe of this general resource. Vus, the heterogenseosaumples derived from diferent disease-based cohortsncabe meta-analyzed to create a general-purpose branieQTL resource representing adult gene regulation, despeitcomprising samples with diferent disease backgronuds, along with normal controls. Verefore, these eQTlLl bwei useful both within and outside these specifdcisease contexts. For example, since these eQTL are not deiasse specifc they may be used to understand healthygene expression regulation in the brain, as well as tonfi er colocalization of eQTL signatures with diseraiske for any disease whose tissue etiology is from the brain, since these signatures are refective of normal brainartieogunl. It should be stated that while many eQTL are not disesae specifc, i.e. they are identifed under various central nervous system (CNS) disease diagnoses and in control brains, they may still contribute to common CNeaSsedsisas previously demonstrate2d4,32–34,45,46. While we have demonstrated a proof-of-concept colocalization analysis with a previously published schizophrenia GWAS, these eQTL are a broadly useful resource for studying nepusryochiatric and neurodegenerative disorders, as well as for understanding the landscape of gene raetgiounl in brain. Methods RNA-seq Re-alignment. For the CMC studies (MSSM-Penn-Pitt, HBCC), RNA-seq reads were aligned to GRCh37 with STAR v2.4.0g159 from the original FASTQ fles. Uniquely mapping rdesa overlapping genes were counted with featureCounts v1.56.02using annotations from ENSEMBL v75.

For the AMP-AD studies (ROSMAP, Mayo RNAseq), Picadr v2.2.4 (https://broadinstitute.github.io/picard)/ was used to generate FASTQ fles from the availablBeAM fles, using the Picard SamToFastq function. Paircd SortSam was frst applied to ensure that R1 and R2erads were correctly ordered in the intermediate SAMfle before converting to FASTQ. Ve converted FASTQs ewaerligned to the GENCODE24 (GRCh38) reference genome using STAR v2.5.1b, with twopassMode set Basasic. Gene counts were computed for each sample by STAR by setting quantMode as GeneCounts.

RNA-seq normalization. To account for diferences between samples, studieesx,perimental batch efects and unwanted RNA-seq-specifc technical variations,we performed library normalization and covariatejuasdtments for each study separately using fxed/mixed efects modeling. A mixed efect model was required to jointly normalize both tissues from the Mayo cohort. All other cohorts contained only one tissueed,seofeactfmxodel was used. Ve workfow consisted of the following steps: 1. Gene fltering: Out of ~56 K aligned and quantifed genes, only genes showing at least modest expression were used in this analysis. Genes that were expressed more than 1 CPM (read Counts Per Million total reads) in at least 50% of samples in each tissue and diagnosis category were retained for analysis. Addi-tion ally, genes with available gene length and percentage GC content from BioMart December 2016 archive were subselected from the above list. Vis resulted in approximately 14 K to 16 K genes in each study. 2. Calculation of normalized expression values:Sequencing reads were then normalized in two steps. First, conditional quantile normalization (CQ6N1 )was applied to account for variations in gene length and GC content. In the second step, the confdence of sampling abundance was estimated using a weighted linear model using the voom-limma package in biocondu6c2t,6o3.rVe normalized observed read counts, along with the corresponding weights, were used in the following steps. 3. Outlier detection: Based on normalized log2(CPM) of expression values, outlier samples were detected using principal component analysis (PCA64),65 and hierarchical clustering. Samples identifed as outliers using both the above methods were removed from further analysis. 4. Covariate imputation: Before identifying associated covariates, important missing covariates were i-mput ed. Principally, post-mortem interval (PMI), or the latency between death and tissue collection, whisch i frequently an important covariate for the analysis of gene expression from post-mortemsburea,inwatiss imputed for a portion of samples in Mayo RNAseq data for which true values were unavailable. Genomic predictors of PMI were estimated using ROSMAP and MSSM (an additional RNA-seq study available through AMP-AD) samples and were used to impute missing values as necessary. 5. Covariate identifcation: Normalized log2(CPM) counts were then explored to determine which known covariates (both biological and technical) should be adjusted. Except for the HBCC study, we usetedpa- s wise (weighted) fxed/mixed efect regression modeling approach to select the relevant covariatesinhgava signifcant association with gene expression. Here, covariates were sequentially added to the model iyf the were signifcantly associated with any of the top principal components, explaining more than 1% oi- f var ance of expression residuals. For HBCC, we used a model selection based on Bayesian informationacriteri (BIC) to identify the covariates that improve the model in more than 50% of genes. 6. SVA adjustments: Ager identifying the relevant known confounders, hidden-confounders were identifed using the Surrogate Variable Analysis (SV4A1.)We used a similar approach as previously defne2d4 to fnd the number of surrogate variables (SVs), which is more conservative than the default method provided by the SVA package in R66. Ve basic idea of this approach is that for an eigenvector decomposition of-permut ed residuals each eigenvalue should explain an equal amount of the variation. By the nature of eig-enval ues, however, there will always be at least one that exceeds the expected value. Vus, from a series of 100 permutations of residuals (white noise) we identifed the number of covariates as shown in Supplemryenta Table 1. We applied the <irw= (iterative re-weighting) version of SVA to the normalized gene expression matrix, along with the covariate model described above to obtain residual gene expression for eQTL analysis. 7. Covariate adjustments: We performed a variant of fxed/mixed efect linear regression, choosing mixed-efect models when multiple tissues or samples, were available per individual, as shown here: gen expression ~ Diagnosi+s Sex + covariates+ (1|Donor), where each gene was linearly regressed ind-e pendently. Here Donor (individual) was modeled as a random efect when multiple tissues from the same individual were present. Observation weights (if any) were calculated using the voom-lim6m2,6a3 pipeline, which has a net efect of up-weighting observations with inferred higher precision in the linear model ftting process to adjust for the mean-variance relationship in RNA-seq data. Ve diagnosis conmenptowas then added back to the residuals to generate covariate-adjusted expression for eQTL analysis.

Vis workfow was applied separately for each study. For the AMP-AD studies, gene locations were liged over to GRCh37 for comparison with the genotype imputation panel (described below). For HBCC, samipthleasgwe <18 were excluded prior to analysis. Supplementary Table 1 shows the covariates and surrogate varleiasbidentifed in each study.

AD diagnosis harmonization. Prior to RNA-seq normalization, we harmonized thOe ALD defnition across AMP-AD studies. AD controls were defned asaptients with a low burden of plaques and tangless, awell as lack of evidence of cognitive impairment. For the ROSMAP study, we defned AD cases to be individuals with a Braak67 greater than or equal to 4, CERAD sco6r8eless than or equal to 2, and a cognitive diagnosis of probable AD with no other causes (cogd=x4), and controls to be individuals with Braak lestshan or equal to 3, CERAD score greater than or equal to 3, and cognitivegdniaosis of 8no cognitive impairment9 (c=og1)d.xFor the Mayo Clinic study, we defned disease status based on neuropathology, where individuals with Braak sceogreater than or equal to 4 were defned to be AD cases, and indiidvuals with Braak less than or equal to 3 were defend to be controls. Individuals not meeting A<D case= or c<ontrol= criteria were retained for anyaslis, and were categorized as o<ther= for the purposes of RNA-seq adjustment.

Genotype QC and imputation. Genotype QC was performed using PLINK v16.99. Markers with zero alternate alleles, genotyping call rate≤ 0.98, Hardy-Weinberg p-value < 5e−5 were removed, as well as individuals with genotyping call rate< 0.90. Samples were then imputed to HRC (Version r1.1 201462)as follows: marker positions were liged-over to GRCh37, if necessaMrya.rkers were then aligned to the HRC loci using HR-C 1000G-check-bim-v4.2 (http://www.well.ox.ac.uk/~wrayner/tool)s,/which checks the strand, alleles, position, reference/alternate allele assignments and frequenices of the markers, removing A/T & G/C single nucoletide polymorphisms (SNPs) with minor allele frequency (AMF) > 0.4, SNPs with difering alleles, SNPs with > 0.2 allele frequency diference between the genotyped samples and the HRC samples, and SNPs not in the reference panel. Imputation was performed via the Michigan Ipmutation Server70 using the Eagle v2.371 phasing algorithm. Imputation was done separately by cohort and by chip within cohort, and markers wi2th≥R0.7 and minor allele frequency (MAF)≥ 0.01 (within cohort) were retained for analysis.

Genetic ancestry inference. GEMTOOLs72 was used to infer ancestry and compute ancestry components separately by cohort. Ve GEMTOOLs algorithm usessaignifcance test to estimate the number of eigenvteocrs (ancestry components) necessary to represent the variability in the da7t3a. For each cohort, we used the top c o-m ponents as estimated by the GEMTOOLs algorithm, whchi resulted in some variation in the number of coom-p nents selected. For MSSM-Penn-Pitt and HBCC, whichare multi-ethnic cohorts, only Caucasian samples wre retained for eQTL analysis. eQTL analysis. eQTL were generated separately in each cohort and tissue using MatrixEQT7L4adjusting for harmonized Diagnosis and inferred Ancestry compontseunsing c<is= gene-marker comparisons: Expression~ Genotype+ Diagnosis+ PC1 + … + PCn,, where PCk is the kth ancestry component, using Expression variables which were previously covariate adjusted as descriebd above. Here we defne c<is= as ± 1 MB around the gene, and GRCh37 gene locations were used for consistenwciyth the marker imputation panel. Meta-analysis was performed via fxed-efect mod7e5lusing an adaptation of the metareg function in the gap package in R. In order to assess potential infation of Type 1 error, wrefpoermed 5 permutations of the gene expression vsa,lureelative to genotype and ancestry components, within diagnisofsor each cohort, and repeated the regression laynsaes as described above. For each of the 5 iterations orfmpuetation, a meta-analysis was then performed acrostshe 4 cohorts. We found that Type 1 error was well conlletrdo(Fig. 1a). Given that multiple tissues were present, we also evaluated a random-efect model, but found substantially defated p-values (less signifcant) in the permautitons, relative to the expected distribution, suggesting that this model is over-conserva.tive Comparison with GTEx and fetal eQTL. Full summary statistics for the GTEx v271 eQTL for all available brain regions were obtained from the GTEx Porthatltp(s://gtexportal.or g),/and fetal eQTL were obtained from Figshare76. For each replication comparison (e.g. meta-anailsyvss GTEx or meta-analysis vs. fetal eQTL), only markers and genes present in both the external eQTL and our analysis were retained for comparni.sAos this was done separately for GTEx and for the fetal eQTL resource, the list of genes and SNPs varies slightly for ea-ch com parison. Ve replication rate was estimated as theπ1 statistic using the qvalue package77 in R as follows: we extracted the meta-analysis p-values for all SNP-gnee pairs, which were signifcant in GTEx at FDR ≤ 0.05. We then applied the 8qvalue9 command to the meta-anasilys p-values to generateπ1 = 1 − π0, which corresponds to estimated proportion of non-null p-va7l7u.eVse 8smoother9 option was used to estimπ0ataes a function of the tuning parameter λ as it approaches 1. Ve variance around this estimtae is relatively small (see Supplementary Figures 1 and 2 for example) and does not materially afect the observations in this manuscript.

Conversely, we estimated the replication rate ofgsniifcant meta-analysis eQTL SNP-gene pairs in GTEx. Analogous methods were used to estimate all otheprlrication rates. For the purposes of reportingttohetal number of eQTL not present in GTEx, and genes withuoteQTL in GTEx (Table 1), we have included genes and SNP-gene pairs not present in GTEx in the count, hwoever this accounts for a relatively small propoornti of the diference (472,995 eQTL and 1481 genes).

GTEx eQTL generation. In order to verify that the observed power increasned replication imbalances were not due to methodological diferences betwehenistmanuscript and those performed by GTEx, we obi ntaed access to the GTEx v7 data, and generated eQTL focrortex, anterior cingulate cortex, and frontal ceoxrutsing our approach. We used gene expression and imputedengotypes as provided, as well as the provided coviatres, which included 3 ancestry covariates, 14-15 surrogtae variable covariates, sex and platform. We thenepreated the comparisons with the meta-analysis described inthe previous section, using a MAF cutof of 0.03h,iwch best appeared to control Type 1 error, as observed by permutation between genotype and geneesesxiporn, while maximizing the number of signifcant eQTL in the true data. Results did not change materially. Pathway analysis of cerebellar eQTL genes. In order to identify whether genes showing cerebellar-specifc eQTL patterns showed any biolocgail coherence, we performed a pathway analysis asof-l lows. For genes with at least 5 signifcant cerebealrl eQTL, we computed the Spearman correlation ofeecft-size between cerebellum eQTL and cortical eQTL for theolci that were signifcant in cerebellum. We then seelcted genes for which the efect-sizes did not show positive correlation (Spearmρa<n90s.1) between the two tissues as showing diferent eQTL association patterns across the gene and performed a pathway analysihs wGiOt biolo-g ical processes Fisher9s exact test. Note that dueot the (power-mediated) greater detection of eQTLcoinrtex, we did not perform the reverse comparison. Ve results were relatively robust to the choice of umminni mumber of signifcant eQTL, correlation cutof, and choice of correlation statistic (Spearman vsoPena)r.s Coloc analysis. We applied Approximate Bayes Factor colocalizati o(cnoloc.abf7 )from the coloc R package to the summary statistics from the PGC2 Schizophrenia GWA36Sdownloaded from the PGC websithet(tp://pgc. unc.edu), and the summary statistics from the eQTL meta-analysis. Each gene present in the meta-analysis was compared to the GWAS in turn, and suggestive andgsinifcant GWAS peaks withp-value < 5e-6 were considered for analysis.

Data availability Data for the ROSMAP37 and Mayo cohor4t0sare available through the AMP-AD Knowledge Por3t1a.lData for the MSSM-Penn-Pitt and HBCC cohorts are available through the CommonMind Knowledge P2o3.rtal eQTL results for the ROSMAP78, Mayo TCX79, Mayo CER80 and cortical meta-analysis81 are available through the AMP-AD Knowledge Portal. Vese results includeNSP (location, rsid, alleles, and allele frequencya)nd gene (location, gene symbol, strand and biotype)foinrmation, as well as estimated efect size (beta)s,tatistic (z), p-value, FDR, and expression-increasing allele.

Code availability An R package with all code for the gene expressionnormalization is available athttps://github.com/SageBionetworks/ampad-difex.pAll other analyses were generated using packagespublicly available from their respective authors.

Acknowledgements For the ROSMAP and Mayo RNAseq studies, the resultspublished here are in whole or in part based on dtaa obtained from the AMP-AD Knowledge Portal (doi:3103.7/syn2580853). ROSMAP study data were provided by the Rush Alzheimer9s Disease Center, Rush University Medical Center, Chicago. Data collection wauspsported through funding by NIA grants P30AG10161, R01AG15891, R01AG17917, R01AG30146, R01AG36836, U01AG32984, U01AG46152, the Illinois Department oPfublic Health, and the Translational Genomics Reserach Institute. Mayo RNA-seq study data were provided bythe following sources: Ve Mayo Clinic AlzheimerseDasie Genetic Studies, led by Dr. Nilufer Ertekin-Taner and Dr. Steven G. Younkin, Mayo Clinic, Jacksonville, FL using samples from the Mayo Clinic Study of Aging, theyMoaClinic Alzheimer9s Disease Research Center, andthe Mayo Clinic Brain Bank. Data collection was suppoedrtthrough funding by NIA grants P50 AG016574, R01 AG032990, U01 AG046139, R01 AG018023, U01 AG006576, U01 AG006786, R01 AG025711, R01 AG017216, R01 AG003949, NINDS grant R01 NS080820, CurePSP Foundation, and support from Mayo Foundation. Study data includes samples collected through the Sun Health Research Institute Brain and Body Dnoation Program of Sun City, Arizona. Ve Brain and Body Donation Program is supported by the National Intestoituf Neurological Disorders and Stroke (U24 NS072026 National Brainnad Tissue Resource for Parkinsons Disease and Reeladt Disorders), the National Institute on Aging (P30 A1G9610 Arizona Alzheimers Disease Core Center), theArizona Department of Health Services (contract 211002, Azroina Alzheimers Research Center), the Arizona Biomdeical Research Commission (contracts 4001, 0011, 05-901nad 1001 to the Arizona Parkinson9s Disease Consoumrt)i and the Michael J. Fox Foundation for ParkinsonseRaerch. Vis study was in part supported by NIH RF1 AG051504 and R01 AG061796 (NET). For CommonMind, dtaa were generated as part of the CommonMind Consortium supported by funding from Takeda Pharemuaticcals Company Limited, F. Hofmann-La Roche Ltd and NIH grants R01MH085542, R01MH093725, P50MH066392, P50MH080405, R01MH097276, RO1-MH-075916, P50M096891, P50MH084053S1, R37MH057881, AG02219, AG05138, MH06692, R01MH110921, R01MH109677, R01MH109897, U01MH103392, and contract HHSN271201300031C through IRP NIMH. Brain tissue for the study was obtainedrof m the following brain bank collections: the MoSiunnati NIH Brain and Tissue Repository, the University oPfennsylvania Alzheimer9s Disease Core Center, the University of Pittsburgh NeuroBioBank and Brain and Tissue Roepsitories, and the NIMH Human Brain Collection C o.re CMC Leadership: Panos Roussos, Joseph Buxbaum, Anedwr Chess, Schahram Akbarian, Vahram Haroutunian (Icahn School of Medicine at Mount Sinai), BernievDlin, David Lewis (University of Pittsburgh), Raqeul Gur, Chang-Gyu Hahn (University of Pennsylvania), EnricoDomenici (University of Trento), Mette A. PeterSso,lveig Sieberts (Sage Bionetworks), Vomas Lehner, Geetha Senthil,eSftano Marenco, Barbara K. Lipska (NIMH). SKS, TP, KKD, JE, AKG, LO, BAL, and LMM were additionalyl supported by NIA grants U24 AG61340, U01 AG46170, U01 AG 46161, R01 AG46171, R01 AG 46174. All data used in this manuscript have been previously released through their respective consortia and have beenvrieewed by IRBs at their institution of origin. Inrmfoed consent has been obtained from all individuals.

Competing interests Ve authors declare no competing interests.

Additional information Supplementary information is available for this paper ahtttps://doi.org/10.1038/s41597-020-00642-.8 Correspondence and requests for materials should be addressed to S.K.S. or L.M.M.

Reprints and permissions information is available at www.nature.com/reprints.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional aoliations.

Open Access This article is licensed under a Creative CommonsAttribution 4.0 International License, which permits use, sharing, adaptation, dsitribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to- the Cre ative Commons license, and indicate if changes werme ade. Ve images or other third party material inhtis article are included in the article9s Creative Commons license, unless indicated otherwise in a crediltine to the material. If material is not included in the article9s Creative Commons license and your intended use is no-t per mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, vhitstipt://creativecommons.org/licenses/by/4.0/ © Ve Author(s) 2020 The CommonMind Consortium (CMC) Schahram Akbarian11, Jaroslav Bendl12, Michael S. Breen13, Kristen Brennand12, Leanne Brown11, Andrew Browne12,14, Joseph D. Buxbaum12,13,14, Alexander Charney12, Andrew Chess15,16,17, Lizette Couto11, Greg Crawford18,19, Olivia Devillers11, Bernie Devlin20, Amanda Dobbyn12,21, Enrico Domenici 22, Michele Filosi 22, Elie Flatow 11, Nancy Francoeur 21, John Fullard12,21, Sergio Espeso Gil 11, Kiran Girdhar 12, Attila Gulyás-Kovács 16, Raquel Gur23, ChangGyu Hahn24, Vahram Haroutunian12,17, Mads Engel Hauberg12,25, Laura Huckins12, Rivky Jacobov11,Yan Jiang11,JessicaS.Johnson 12,BibiKassim 11,YungilKim 12,LambertusKlei 20, Robin Kramer26, Mario Lauria27, Thomas Lehner28, David A. Lewis20, Barbara K. Lipska26, Kelsey Montgomery1, Royce Park11, Chaggai Rosenbluh16, Panagiotis Roussos11,14,15,29, Douglas M. Ruderfer30, Geetha Senthil28, Hardik R. Shah 14, Laura Sloofman 12, Lingyun Song18, Eli Stahl12, Patrick Sullivan31, Roberto Visintainer22, Jiebiao Wang32,Ying-Chih Wang15, Jennifer Wiseman11, Eva Xia 21, Wen Zhang12 & Elizabeth Zharovsky 11 11Division of Psychiatric Epigenomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA1.2Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA13.Seaver Autism for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, U1S4FAr.iedman Brain Institute, Icahn School of Medicine at Mount Sinai, NewYork, NewYork, US A15.Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NewYork, NewYork, U1S6DAe. partment of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 17Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New YNoerwkY,ork, USA.18Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, 1U9DSAiv.ision of Medical Genetics, Department of Pediatrics, Duke University, Durham, North Carolina, US2A0D. epartment of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, US21AD.epartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NewYork, NewYork, USA22.Laboratory of Neurogenomic Biomarkers, Centre for Integrative Biology (CIBIO), University of Trento, Trento,23INtaelyu.ropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Pheilpahdia, Pennsylvania, USA. 24Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA. 25Department of Biomedicine, Aarhus University, Aarhus, Denmark. 26Human Brain Collection Core, National Institutes of Health, NIMH, Bethesda, Maryland, US2A7D.epartment of Mathematics, University of Trento, Trento, Ita2l8yN. ational Institute of Mental Health, Bethesda, Maryland, USA. 29Psychiatry, JJ Peters VA Medical Center, Bronx, New York, USA3.0Department of Medicine, Psychiatry and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt Univertsyi Medical Center, Nashville, Tennessee,

1. Zhu , Z. et al. Integration of summary data from GWAS and eQTLudsites predicts complex trait gene targetsN . at. Genet . 48 , 481 - 487 ( 2016 ). 2. Nica , A. C. et al. Candidate Causal Regulatory Efects by Integration of Expression QTLs with Complex Trait GenetiscoAcsiations . PLoS Genet 6 , e1000895 ( 2010 ). 3. Ongen , H.et al. Estimating the causal tissues for complex traits and diseaseNs . at. Genet . 49 , 1676 - 1683 ( 2017 ). 4. Chun , S. et al. Limited statistical evidence for shared geneticfeects of eQTLs and autoimmune-disease-associatedclioin three major immune-cell types . Nat. Genet . 49 , 600 - 605 ( 2017 ). 5. Hormozdiari , F. , Kostem , E. , Kang , E. Y. , Pasaunci , B. & Eskin , E. Identifying Causal Variants at oL ci with Multiple Signals of AssociationG .enetics 198 , 497 - 508 ( 2014 ). 6. He , X. et al. Sherlock: Detecting Gene-Disease Associations bMy atching Patterns of Expression QTL and GWASA.m. J. Hum. Genet . 92 , 667 - 680 ( 2013 ). 7. Giambartolomei , Ce.t al. Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using SummarsytiSctsa . ti PLoS Genet 10 , e1004383 ( 2014 ). 8. Gamazon , E. R. et al. A gene-based association method for mapping tsrauisting reference transcriptome dataN . at. Genet . 47 , 1091 - 1098 ( 2015 ). 9. Barbeira , A. N. et al. Exploring the phenotypic consequences of tissupe csifc gene expression variation inferred from GWAS summary statistics . Nat. Commun. 9 , 1825 ( 2018 ). 10. Zhu , J. et al. An integrative genomics approach to the reconsctrtiuon of gene networks in segregating populatioCyntso.genet . Genome Res . 105 , 363 - 74 ( 2004 ). 11. Schadt , E. et al. Mapping the Genetic Architecture of Gene Expression in Human LivePr.LoS Biol 6 , e107 ( 2008 ). 12. Zhu , J. et al. Integrating large-scale functional genomic daota tdissect the complexity of yeast regulatory netwkso . Nrat. Genet . 40 , 854 - 61 ( 2008 ). 13. Greenawalt , D. M. et al. A survey of the genetics of stomach, liver, anddipaose gene expression from a morbidly obese co . hort Genome Res . 21 , ( 2011 ). 14. Zhang , B. et al. Integrated systems approach identifes genetic noeds and networks in late-onset Alzheimer9s diseaseC . ell 153 , 707 - 20 ( 2013 ). 15. Franzén , O. et al. Cardiometabolic risk loci share downstream cisn-da trans-gene regulation across tissues and diseas . eScience 353 , 827 - 30 ( 2016 ). 16. Peters , L. A. et al. A functional genomics predictive network model identifes regulators of infammatory boweel . dNisaeta.sGenet. 49 , 1437 - 1449 ( 2017 ). 17. Battle , A. et al. Characterizing the genetic basis of transcriptomdeiversity through RNA-sequencing of 922 individusa . Glenome Res 24 , 14 - 24 ( 2014 ). 18. Westra , H.-J. et al. Systematic identifcation of trans eQTLs as putavtei drivers of known disease associationNsa . t. Genet . 45 , 1238 - 1243 ( 2013 ). 19. Võsa , U. et al. Unraveling the polygenic architecture of complterxaits using blood eQTL meta-analysisb.ioRxiv Preprint at , http:// biorxiv.org/content/early/2018/10/19/447367.abstra( c2t018 ). 20. Qi , T. et al. Identifying gene targets for brain-related traits using transcriptomic and methylomic data froomdb . Nloat. Commun . 9 , 2282 ( 2018 ). 21. Aguet , F. et al. Genetic efects on gene expression across human tissueNs.ature 550 , 204 - 213 ( 2017 ). 22. Ardlie , K. G. et al. Ve Genotype-Tissue Expression ( GTEx) pilot analiyss: Multitissue gene regulation in humansS.cience (80- .) 348 , 648 - 660 ( 2015 ). 23. CommonMind Consortium Data Release PorStayln .apse https://doi.org/10.7303/syn275979(22015). 24. Fromer , M. et al. Gene expression elucidates functional impact ofoplygenic risk for schizophreniNaa . ture Neuroscience 19 , 1442 - 1453 ( 2016 ). 25. Wang , D. et al. Comprehensive functional genomic resource andeginrtative model for the human brainSc . ience (80-.) . 362 , eaat8464 ( 2018 ). 26. Hofman , G. E. et al. CommonMind Consortium provides transcriptomic aenpdigenomic data for Schizophrenia and Bipolar Disorder . Sci. Data 6 , 180 ( 2019 ). 27. Chibnik , L. B. et al. Susceptibility to neurofibrillary tangles: rolef othe PTPRD locus and limited pleiotropy with other neuropathologieMs . ol. Psychiatry 23 , 1521 ( 2017 ). 28. Mostafavi , Se.t al. A molecular network of the aging human brain pridoevs insights into the pathology and cognitive dinecelof Alzheimer9s disease . Nat. Neurosci . 21 , 811 - 819 ( 2018 ). 29. Allen , M. et al. Human whole genome genotype and transcriptome data for Alzheimer9s and other neurodegeenedriasetiavses . Sci. Data 3 , 160089 ( 2016 ). 30. Wan , Y.W. et al. Meta-Analysis of the Alzheimer9s Disease Human Barin Transcriptome and Functional Dissection in Moeus Models . C ell Rep . 32 ( 2 ), 107908 ( 2020 ). 31. AMP AD Target Discovery Data PortaSl .ynapse https://doi.org/10.7303/syn258085(32015). 32. Allen , M. et al. Novel late-onset Alzheimer disease loci variants associate with brain gene expressioNneu . rology 79 , 221 - 8 ( 2012 ). 33. Zou , F. et al. Brain expression genome-wide association studyG(WeAS) identifes human disease-associated variants . PLoS Genet 8 , e1002707 ( 2012 ). 34. Allen , M. et al. Late-onset Alzheimer disease risk variants mark brain regulatory locNi . eurol. Genet . 1 , e15 ( 2015 ). 35. Ng , B. et al. An xQTL map integrates the genetic architecture of the human brain9s transcriptome and epigeno . Nmaet. Neurosci . 20 , 1418 - 1426 ( 2017 ). 36. Ripke , S. et al. Biological insights from 108 schizophrenia-associated genetic Nloatcui.re 511 , 421 - 427 ( 2014 ). 37. ROSMAP Study . Synapse https://doi.org/10.7303/syn321904(52016). 38. Allen , M. et al. Conserved brain myelination networks are altereidn Alzheimer9s and other neurodegenerative diseas . eAs lzheimers. Dement . 14 , 352 - 366 ( 2018 ). 39. Allen , M. et al. Divergent brain gene expression patterns associeatwith distinct cell-specifc tau neuropathology tirtas in progressive supranuclear palsy . Acta Neuropathol 136 , 709 - 727 ( 2018 ). 40. Mayo RNAseq Study.Synapse https://doi.org/10.7303/syn555040(42016). 41. Leek , J. T. & Storey , J. D. Capturing Heterogenitey in Gene Expression Studies by Surrogate VariaebAlnalysis . Plos Genet 3 , e161 ( 2007 ). 42. McCarthy , S. et al. A reference panel of 64,976 haplotypes for genotype imputatNioatn .. Genet . 48 , 1279 - 83 ( 2016 ). 43. O9Brien, H. E. et al. Expression quantitative trait loci in the develoinpg human brain and their enrichment in neuropsychiatric disorders . Genome Biol 19 , 194 ( 2018 ). 44. Hou , Y. et al. Schizophrenia-associated rs4702 G allele-specifcdownregulation of FURIN expression by miR-338-3dpurcees BDNF productionS . chizophr. Res . 199 , 176 - 180 ( 2018 ). 45. Dobbyn , A. et al. Landscape of Conditional eQTL in DorsolateralfProrental Cortex and Co-localization with SchizopiharGenWAS . Am. J. Hum. Genet . 102 , 1169 - 1184 ( 2018 ). 46. Pardiñas , A. F. et al. Common schizophrenia alleles are enriched in mutiaon-intolerant genes and in regions under strong background selectionN . at. Genet . 50 , 381 - 389 ( 2018 ). 47. Liu , Y. et al. Non-coding RNA dysregulation in the amygdala roegni of schizophrenia patients contributes to thehpoagtenesis of the disease . Transl. Psychiatry 8 , 44 ( 2018 ). 48. Lu , A. T. et al. Genetic architecture of epigenetic and neuronal ageing rates in human brain regioNnas . t. Commun . 8 , 15353 ( 2017 ). 49. Davies , M. N. et al. Functional annotation of the human brain methylome identifes tissue-specifc epigenetic variation acroisns bra and bloodG . enome Biol 13 , R43 ( 2012 ). 50. Hannon , E. , Lunnon , K. , Schalkwyk , L. & Mill, JI.nterindividual methylomic variation across bloocdo,rtex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenoEtyppigeesn . etics 10 , 1024 - 1032 ( 2015 ). 51. Guintivano , J. , Aryee , M. J. & Kaminsky , Z. A. Acell epigenotype specifc model for the correctioofnbrain cellular heterogeneity bias and its application to age, brain region and major depressi oEpni . genetics 8 , 290 - 302 ( 2013 ). 52. Negi , S. K. & Guda , C. Global gene expression porfling of healthy human brain and its application situdying neurological disorders . Sci. Rep . 7 , 897 ( 2017 ). 53. Azevedo , F. A. C. et al. Equal numbers of neuronal and nonneuronal cellaskme the human brain an isometrically scaled-up primate brain . J. Comp. Neurol . 513 , 532 - 541 ( 2009 ). 54. Ma , S. , Hsieh , Y.-P. , Ma , J. & Lu , C. Low-inputand multiplexed microfuidic assay reveals epigenomcivariation across cerebellum and prefrontal cortexS.ci . Adv . 4 , eaar8187 ( 2018 ). 55. Westra , H.-J. et al. Cell Specifc eQTL Analysis without Sorting CellsP.los Genet 11 , e1005223 ( 2015 ). 56. van der Wijst , M. G. P. et al. Single-cell RNA sequencing identifes celltype-specifc cis-eQTLs and co-expression QTLNs .at. Genet . 50 , 493 - 497 ( 2018 ). 57. Wang , J. , Devlin , B. & Roeder , K. Using multiplemeasurements of tissue to estimate individual- andcell-type-specific gene expression via deconvolutiobni . oRxiv 379099 , https://doi.org/10.1101/37909(92018). 58. Li , M. et al. Integrative functional genomic analysis of humbarnain development and neuropsychiatric risksS . cience (80-.) . 362 , eaat7615 ( 2018 ). 59. Dobin , A. et al. STAR: ultrafast universal RNA-seq aligner . Bioinformatics 29 , 15 - 21 ( 2013 ). 60. Liao , Y. , Smyth , G. K. & Shi , W. featureCountsa:n eocient general purpose program for assigningqusence reads to genomic features . Bioinformatics 30 , 923 - 30 ( 2014 ). 61. Hansen , K. D. , Irizarry , R. A. & WU , Z. Removingtechnical variability in RNA-seq data using condiitonal quantile normalization . Biostatistics 13 , 204 - 216 ( 2012 ). 62. Ritchie , M. E. et al. limma powers diferential expression analyses foRrNA-sequencing and microarray studies . Nucleic Acids Res 43 , e47 - e47 ( 2015 ). 63. Law , C. W. , Chen , Y. , Shi , W. & Smyth , G. K. Vomo : precision weights unlock linear model analysiostols for RNA-seq read counts . Genome Biol . 15 , R29 ( 2014 ). 64. Pearson , K. LIII. On lines and planes of closefst to systems of points in spacLeo .ndon, Edinburgh, Dublin Philos. Mag. J. Sci 2 , 559 - 572 ( 1901 ). 65. Hotelling , H. Analysis of a complex of statistical variables into principal compoJn . eEndtus.c. Psychol . 24 , 417 - 441 ( 1933 ). 66. Leek , J. T. et al. Bioconductor - svah.,ttps://doi.org/10.18129/B9.bioc. sv(a2018). 67. Braak , H. & Braak , E. Neuropathological stageing of Alzheimer-related chanAgectsa . Neuropathol . 82 , 239 - 259 ( 1991 ). 68. Chandler , M. J. et al. A total score for the CERAD neuropsychological batNteeruyr . ology 65 , 102 - 106 ( 2005 ). 69. Chang , C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasGeitgsa . science 4 , 7 ( 2015 ). 70. Das , S. et al. Next-generation genotype imputation service and methoNdsa. t. Genet . 48 , 1284 - 1287 ( 2016 ). 71. Loh , P. -R.et al. Reference-based phasing using the Haplotype Reference Consortium panNeal . t. Genet . 48 , 1443 ( 2016 ). 72. Klei , L. , Kent , B. P. , Melhem , N. , Devlin , B. & Roeder , K. GemTools: A fast and eocient approachetsotimating genetic ancestry . ( 2011 ). 73. Lee , A. B. , Luca , D. , Klei , L. , Devlin , B. & Roeder , K. Discovering genetic ancestry using spectral graph theoGrye . net. Epidemiol . 34 , 51 - 59 ( 2010 ). 74. Shabalin , A. A. Matrix eQTL: ultra fast eQTL analysis via large matrix operationBs . ioinformatics 28 , 1353 - 1358 ( 2012 ). 75. Begum , F. , Ghosh , D. , Tseng , G. C. & Feingold ,. EComprehensive literature review and statistical considerations for GWAS metaanalysis . Nucleic Acids Res 40 , 3777 - 3784 ( 2012 ). 76. O9Brien, H. & Bray , N. J. Summary statistics foerxpression quantitative trait loci in the develonpgi human brain and their enrichment in neuropsychiatric disordersF .igshare https://doi.org/10.6084/m9.fgshare. 6881825 .v( 12018 ). 77. Storey , J.D. , Bass , A.J. , Dabney , A. & RobinsonD, .  qvalue: Q-value estimation for false discovery rate control http://github .com/ jdstorey/qvalue( 2020 ). 78. Sieberts , S. ROSMAP DLPFC eQTL . Synapse https://doi.org/10.7303/syn16984409.( 12019 ). 79. Sieberts , S. Mayo Temporal Cortex eQTLS .ynapse https://doi.org/10.7303/syn16984410.( 12019 ). 80. Sieberts , S. Mayo Cerebellum eQTL .Synapse https://doi.org/10.7303/syn16984411.( 12019 ). 81. Sieberts , S. Cortical eQTL Meta-analysis .Synapse https://doi.org/10.7303/syn16984815.( 12019 ). Author contributions S.K.S ., S.M. , M.P. , P.L.D.J. , N.E.T. and L.M. M., the AMP-AD Consortium, and the CMC Consortium conturtiebd to the design and generation of the study data. S.S.K ., T.P. , M.C., M.A. , J.S.R. , G.H. , K.D.D. , J.C. , P.J.E. and J.E. contributed the data analysis. S.K.S ., T.P. , G.H. , A.K.G. , L.O. , M.P. , B.A.L. , L.M. M. contributed to the manuscript preparation and data sharing .