Data for "Brain cell-type shifts in Alzheimer's disease, autism and schizophrenia interrogated using methylomics and genetics"

<p>Data for &quot;Genetic and methylomic interrogation of brain cell-type shifts in autism, schizophrenia, and Alzheimer&rsquo;s disease&quot; (Yap et al. 2023).</p> <p>Source data from ROSMAP, LIBD and UCLA_ASD post-mortem brain datasets.</p> <p>This data repository contains 3 files:</p> <p><strong>220819_Supplementary_Tables.xlsx</strong></p> <p>Supplementary Tables for the manuscript:</p> <ol> <li>Supplementary Table 1: Comparison of CTP deconvolution methods in the ROSMAP dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled &quot;unknown1&quot;); VAEe* indicates variational autoencoder embeddings.</li> <li>Supplementary Table 2: Comparison of CTP deconvolution methods in the LIBD dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled &quot;unknown1&quot;); VAEe* indicates variational autoencoder embeddings.</li> <li>Supplementary Table 3: Comparison of CTP deconvolution methods in the UCLA_ASD dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequencing reference data; celfie* indicates CelFIE (and includes an output titled &quot;unknown1&quot;); VAEe* indicates variational autoencoder embeddings.</li> <li>Supplementary Table 4: Deconvolved brain CTPs (raw), with covariates.</li> <li>Supplementary Table 5: Deconvolved brain CTPs (clr-transform, offset 1e-3), with covariates and raw PGS for all ancestries. Comp* indicates compositionally-aware principal components of the CTP data; *pgs_raw indicates PGS calculated for using genotyping across all ancestries. This table has a total of n=1,098 across all ancestries, including n=885 EUR. After applying a rel&lt;0.05 threshold on the n=885 EUR, there were n=878 EUR which were used in the PGS analysis so that population stratification PCs did not simply capture family structure.</li> <li>Supplementary Table 6: Deconvolved brain CTPs (clr-transform, offset 1e-3), with covariates and standardised PGS for n=878 Europeans. *pgs_raw indicates unstandardised PGS, PC* indicates genotyping PCs within the European dataset, *_PGS indicates standardised PGS within the European subset.</li> <li>Supplementary Table 7: Deconvolved brain CTPs (clr-transform, offset 1e-3), adjusted for oligodendrocyte proportions, with covariates.</li> <li>Supplementary Table 8: Deconvolved brain CTPs (raw), adjusted for oligodendrocyte proportions, with covariates.</li> </ol> <p><strong>20220108_maf05_gwas_ctp.tar.gz</strong></p> <p>GWAS summary statistics for the 7 brainCTPs (clr-transformed): Exc, Inh, Astro, Endo, Micro, Oligo, OPC</p> <p>METAL output format:<br> MarkerName: SNP<br> Allele1<br> Allele2<br> Freq1: Allele1 frequency<br> FreqSE: frequency standard error<br> MinFreq: minimum Allele1 frequency in meta-analysis<br> MaxFreq: maximum Allele1 frequency in meta-analysis<br> Effect: effect size<br> StdErr: standard error of effect size<br> P-value: calculated in inverse variance weighted meta-analysis<br> Direction: directions of effects across the 3 datasets<br> HetISq: heterozygosity I-squared<br> HetChiSq: heterozygosity chi-squared<br> HetDf: heterozygosity degress of freedom<br> HetPVal: heterozygosity test p-value</p> <p><strong>20220108_maf05_gwas_ctp_pc.tar.gz</strong></p> <p>GWAS summary statistics for the 5 CTP_PCs</p> <p>METAL output format (see above)</p> <p>&nbsp;</p> <p><strong>Source data</strong>:</p> <p>ROSMAP: Raw methylation .idat files were obtained from Synapse accession syn7357283. Whole genome sequencing .vcf files (variants jointly called with MSBB and Mayo studies) were obtained from Synapse accession syn11707420.</p> <p>LIBD: Raw methylation .idat files were obtained from GEO accession GSE74193. SNP genotypes were downloaded from dbGaP accession phs000417.v2.p1.</p> <p>UCLA-ASD: The processed methylation beta matrix was downloaded from Synapse accession syn8263588. SNP genotypes were downloaded from Synapse accession syn10537134.</p> <p>GWAS summary statistics are available at: 10.5281/zenodo.7604231</p> <p>Code is available on GitHub: gandallab/brain_CTP_deconv</p>