Publications by Charleen Adams
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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Genetic Correlations between UKB-PPP Chemokines
1 Introduction This analysis uses linkage disequilibrium score regression (LDSC) to obtain genetic correlations (rgs) between Olink chemokines. LDSC requires LD scores (r2) values (vs SuSiE and coloc which use the signed correlation, r). We are starting with the UKB Olink proteins because the Alkes lab has precalcuated LD scores for Europeans. We�...
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SuSiE PCSK9
1 Introduction This analysis investigates the potential genetic overlap between proprotein convertase subtilisin/kexin type 9 (PCSK9) and Body Mass Index (BMI) using summary statistics, SuSiE fine-mapping, and colocalization analysis. We focus on a 500KB region upstream and downstream of the sentinel SNP rs147852470 and include only variants with a...
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Analysis of N-Acetyltaurine and BMI with SuSiE and Colocalization
1 Introduction This analysis investigates the potential genetic overlap between N-acetyltaurine (NAT) and Body Mass Index (BMI) using summary statistics, SuSiE fine-mapping, and colocalization analysis. We focus on a 500KB region upstream and downstream of the sentinel SNP rs147852470. 2 Data Preparation 2.1 Load the Merged Summary Statistics We ...
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