Publications by Charleen Adams
Testing UserGWAS/GenomicSEM for Value with Three Moderately Genetically Correlated Chemokines
1 Bioinformatics Processing: Fetching rsID and Pvals #!/bin/bash # Directories and variables TAR_DIR="/Users/charleenadams/ukbppp/chemokine_list" MAP_DIR="/Users/charleenadams/temp_BI/chemokine_rgs_olink/maps" OUTPUT_BASE_DIR="/Users/charleenadams/temp_BI/chemokine_rgs_olink/processed_ukbppp_chemokine_list" MERGED_DIR="$OUTPUT_BASE_DIR/merged_file...
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Mendelian Randomization of METSIM N-acetylalanine (ACY1 Region) and BMI
1 Instrument Selection # Set working directory setwd("/Users/charleenadams/metsim_nacy1_bmi") # Load ACY1 data acy1 <- fread("phenocode-C1110.tsv") # Retrieve TSS data for ACY1 using Ensembl #ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") ensembl <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", mirror = "use...
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Latent Factor Multivariate `userGWAS` of Selected Proteins
1 Multivariate GWAS In this analysis, we employ a genomic structural equation model (GenomicSEM) to define a new phenotype: a latent factor that influences 12 proteins we know are influenced by a common SNP. 2 Select Proteins Related to Functional Study # Ensure the destination directory exists mkdir -p /Users/charleenadams/ukbppp/selected_set #...
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Fetch 22:30529631:C:A:imp:v1_RPS3AP51_rs2412973 from UKB-PPP
1 Can’t Use Sun Supplementary Table 9 (ST9), BUT Can Extract From Primary Data Sun only provided top SNPs for their most significant results in their Supplemental Table 9 (ST9), not for those of varying P thresholds. But I downloaded the all the primary pQTL files for the EUR discovery set (n = 2940). These are about 1.5 TB compressed (find /User...
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Multivariate `userGWAS` of Four Selected Chemokines: CCL5, CXCL5, CCL8, & CCL7
0.1 Multivariate GWAS In this analysis, we employ a genomic structural equation model (GenomicSEM) to define a new phenotype: a latent factor that influences four CCL5, CXCL5, CCL8, & CCL7. In essence, while the chemokines themselves are directly measurable phenotypes, the latent factor we infer captures the shared genetic influence among these che...
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Multivariate GWAS of 39 Chemokines
1 Multivariate GWAS for Chemokines In this analysis, we employ a genomic structural equation model to define a new phenotype: a latent factor that influences chemokines. In essence, while the chemokines themselves are directly measurable phenotypes, the latent factor we infer captures the shared genetic influence among these chemokines. The GWAS re...
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Chemokines Analysis (2)
1 Introduction This pipeline uses linkage disequilibrium score regression (LDSC) to calculate genetic correlations (rg) between 33 Olink chemokines. 1.1 Note 1 LDSC requires linkage disequilibrium (LD) scores based on r² values, unlike SuSiE and coloc, which rely on the signed correlation coefficient (r) in matrix form. These LD scores are also a...
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Pathway Enrichment Analysis: Exploring Pleiotropy in the UK Biobank Pharma Proteomics Project
1 Introduction Here, we conduct a pathway enrichment analysis to investigate pleiotropy within and across biologically defined pathways for top SNPs identified in the Sun et al. (2023) UK Biobank Pharma Proteomics Project (UKB-PPP) 1. The study’s Supplementary Table 9 (ST9), which we utilized, includes 30,743 significant pQTLs (P < 1.7 × 10⁻¹...
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Chemokines Analysis
1 Introduction This pipeline uses linkage disequilibrium score regression (LDSC) to calculate genetic correlations (rg) between 33 Olink chemokines. 1.1 Note 1 LDSC requires linkage disequilibrium (LD) scores based on r² values, unlike SuSiE and coloc, which rely on the signed correlation coefficient (r) in matrix form. These LD scores are also a...
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Mendelian Randomization of ACY1 and BMI
0.1 Introduction Here we perform a Mendelian randomization (MR) of circulating ACY1 levels on body mass index (BMI) in participants in the UK Biobank (UKB). Our genetic instruments come from UK Biobank Pharma Proteomics Project (UKB-PPP) and our BMI summary statistics come from Jurgens et al. We do so first using three biologically informed SNPs a...
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