8  Sensitivity analyses

8.1 European only analyses

The same Mendelian randomization analyses as in Section 6.2 were performed using European only samples (where available).

# MR analyses
mr_results <- fread(
    "./data/00_data_sensitivity_eur_mr.tsv",
    header = TRUE, data.table = FALSE, sep = "\t"
)
mr_studies <- fread(
    "./data/00_data_sensitivity_eur_mr_studies.tsv",
    header = TRUE, data.table = FALSE, sep = "\t"
)

# MR results
mr_results <- mr_studies %>%
    select(id, pmid, trait, n, n_cases) %>%
    inner_join(
        x = .,
        y = mr_results,
        by = "id"
    )

README

• id - dataset ID
  
• pmid - PubMed ID
  
• trait - phenotype
  
• n - number of samples
  
• n_cases - number of cases
  
• model - MR model
  
• n_snps - number of SNPs
  
• beta - MR effect size (per SD lower sclerostin)
  
• se - MR standard error
  
• pvalue - MR p-value

8.1.1 Results

Associations

Table 8.1: MR results of the effect of per SD lower sclerostin on cardiovascular events and risk factors

: Effect (in SD)
: Odds ratio

QQ plots

Original datasets

2 cis pQTLs

mr_results %>%
    filter(model == "2_cis_pqtls") %>%
    inner_join(
        x = select(mr_studies, id, flag),
        y = .,
        by = "id"
    ) %>%
    filter(flag == "Y") %>%
    distinct(trait, .keep_all = TRUE) %>%
    qq_plot()

Figure 8.1: QQ plot of MR results (2 cis pQTLs) for the original datasets

5 cis pQTLs

mr_results %>%
    filter(model == "5_cis_pqtls") %>%
    inner_join(
        x = select(mr_studies, id, flag),
        y = .,
        by = "id"
    ) %>%
    filter(flag == "Y") %>%
    distinct(trait, .keep_all = TRUE) %>%
    qq_plot()

Figure 8.2: QQ plot of MR results (5 cis pQTLs) for the original datasets

Additional datasets

2 cis pQTLs

mr_results %>%
    filter(model == "2_cis_pqtls") %>%
    inner_join(
        x = select(mr_studies, id, flag),
        y = .,
        by = "id"
    ) %>%
    filter(flag == "N") %>%
    qq_plot()

Figure 8.3: QQ plot of MR results (2 cis pQTLs) for the additional datasets

5 cis pQTLs

mr_results %>%
    filter(model == "5_cis_pqtls") %>%
    inner_join(
        x = select(mr_studies, id, flag),
        y = .,
        by = "id"
    ) %>%
    filter(flag == "N") %>%
    qq_plot()

Figure 8.4: QQ plot of MR results (5 cis pQTLs) for the additional datasets

8.2 UK Biobank sclerostin pQTLs

Genetic variant associations with circulating sclerostin in the SOST region from UK Biobank using the Olink platform were obtained from Sun et al. (2023). Sclerostin pQTLs in cis of SOST (±100KB) were defined using LD clumping using LDlinkR setting \(r^2 < 0.2\) (Myers et al. 2020). Three sclerostin pQTLs were identified rs1513671, rs80107551 (this variant was included in the Zheng et al. (2023) sclerostin pQTLs) and rs865429. These sclerostin pQTLs were used to perform the same Mendelian randomization analyses as in Section 6.2 using the Zheng et al. (2023) sclerostin pQTLs.

source("./scripts/04_data_ukbb_pqtls_region.R")
source("./scripts/05_data_ukbb_pqtls.R")
source("./scripts/06_data_gwas_ukbb_pqtls.R")

8.2.1 Data

# Data
load("./data/01_data_ldmat.Rda")
load("./data/06_data_gwas_ukbb_pqtls.Rda")

# GWAS
gwas <- gwas %>%
    filter(!(id %in% c("GCST006979", "GCST006980")))

8.2.2 Analyses

Mendelian randomization (MR) analyses of circulating sclerostin against cardiovascular events and risk factors were performed using the datasets in Table 2.2. The cis sclerostin pQTLs from UK Biobank were used as the genetic instruments. Since the sclerostin pQTLs are correlated, the generalized inverse-weighted method (Burgess et al. 2016) was used to perform the MR analyses.

# MR analyses
mr_results <- tibble()
for (id in unique(gwas$id)) {
    ## MR data

    ### GWAS
    mr_data <- gwas %>%
        filter(id == !!id) %>%
        inner_join(
            x = pqtls,
            y = .,
            by = c("rsid", "chr", "pos", "ref", "alt")
        ) %>%
        relocate(id, .before = rsid)

    ### LD matrix
    mr_corr <- ld_mat[
        match(mr_data$rsid, rownames(ld_mat)),
        match(mr_data$rsid, rownames(ld_mat)),
        drop = FALSE
    ]
    if (any(mr_data$rsid != rownames(mr_corr))) {
        stop("genetic varaints are not aligned between the GWAS data and the LD matrix")
    }

    ## MR analysis

    ### Input
    mr_inputs <- MendelianRandomization::mr_input(
        bx = mr_data$beta.x,
        bxse = mr_data$se.x,
        by = mr_data$beta.y,
        byse = mr_data$se.y,
        correlation = mr_corr,
        snps = mr_data$rsid
    )

    ### Analysis
    mr_analysis <- MendelianRandomization::mr_ivw(
        mr_inputs,
        model = "fixed",
        correl = TRUE
    )
    mr_analysis <- tibble(
        id = !!id,
        model = "UKBB cis pQTLs",
        n_snps = !!nrow(mr_data),
        beta = -1 * !!round(mr_analysis$Estimate, 6), # per lower SD sclerostin
        se = !!round(mr_analysis$StdError, 6),
        pvalue = !!signif(mr_analysis$Pvalue, 4)
    )

    ### Results
    mr_results <- mr_results %>%
        bind_rows(mr_analysis)
}

# MR results
mr_results <- studies %>%
    select(id, pmid, trait, n, n_cases) %>%
    inner_join(
        x = .,
        y = mr_results,
        by = "id"
    )

README

• id - dataset ID
  
• pmid - PubMed ID
  
• trait - phenotype
  
• n - number of samples
  
• n_cases - number of cases
  
• model - MR model
  
• n_snps - number of SNPs
  
• beta - MR effect size (per SD lower sclerostin)
  
• se - MR standard error
  
• pvalue - MR p-value

8.2.3 Results

Associations

Table 8.2: MR results of the effect of per SD lower sclerostin on cardiovascular events and risk factors

: Effect (in SD)
: Odds ratio

QQ plots

Original datasets

mr_results %>%
    inner_join(
        x = select(studies, id, flag),
        y = .,
        by = "id"
    ) %>%
    filter(flag == "Y") %>%
    distinct(trait, .keep_all = TRUE) %>%
    qq_plot()

Figure 8.5: QQ plot of MR results for the original datasets

Additional datasets

mr_results %>%
    inner_join(
        x = select(studies, id, flag),
        y = .,
        by = "id"
    ) %>%
    filter(flag == "N") %>%
    qq_plot()

Figure 8.6: QQ plot of MR results or the additional datasets

Burgess S, Dudbridge F, Thompson SG. Combining information on multiple instrumental variables in mendelian randomization: Comparison of allele score and summarized data methods. Statistics in medicine. 2016;35(11):1880–906.

Myers TA, Chanock SJ, Machiela MJ. LDlinkR: An r package for rapidly calculating linkage disequilibrium statistics in diverse populations. Frontiers in genetics. 2020;11:157.

Sun BB, Chiou J, Traylor M, et al. Plasma proteomic associations with genetics and health in the UK biobank. Nature. 2023;1–10.

Zheng J, Wheeler E, Pietzner M, et al. Lowering of circulating sclerostin may increase risk of atherosclerosis and its risk factors: Evidence from a genome-wide association meta-analysis followed by mendelian randomization. Arthritis & Rheumatology. 2023;75(10):1781–92.