5  Sclerostin pQTL associations

Genetic associations of the sclerostin pQTLs in the datasets in Table 2.2.

load("./data/03_data_gwas_pqtls.Rda")
gwas <- studies %>%
  select(id, pmid, trait, n, n_cases, flag) %>%
  inner_join(
    x = .,
    y = gwas,
    by = "id"
  )
README
  • id - dataset ID
  • pmid - PubMed ID
  • trait - phenotype
  • n - number of samples
  • n_cases - number of cases
  • rsid - rsID
  • chr - chromosome
  • pos - position (build 37)
  • ref - reference allele
  • alt - alternate allele (effect allele)
  • af - allele frequency of the alternate allele
  • beta - effect size
  • se - standard error
  • pvalue - p-value

5.1 Original datasets

Genetic associations of the sclerostin pQTLs with cardiovascular events and risk factors in the datasets in Table 2.2 that were analysed by Zheng et al. (2023) (or equivalent1).

assoc <- gwas %>%
  filter(flag == "Y" & !(id %in% c("GCST006979", "GCST006980"))) %>%
  select(id, pmid, trait, n, n_cases, rsid, pvalue) %>%
  arrange(pvalue)
Table 5.1: GWAS associations with sclerostin pQTLs (original datasets) 
qq_plot(assoc)
Figure 5.1: QQ plot of GWAS associations with sclerostin pQTLs (original datasets)

5.2 Additional datasets

Genetic associations of the sclerostin pQTLs with cardiovascular events and risk factors in the additional recent GWAS datasets in Table 2.2.

assoc_add <- gwas %>%
  filter(flag == "N") %>%
  select(id, pmid, trait, n, n_cases, rsid, pvalue) %>%
  arrange(pvalue)
Table 5.2: GWAS associations with sclerostin pQTLs (additional datasets) 
qq_plot(assoc_add)
Figure 5.2: QQ plot of GWAS associations with sclerostin pQTLs (additional datasets)

  1. The ischemic and cardioembolic stroke GWAS results from METASTROKE (Malik et al. 2016) used by Zheng et al. (2023) were replaced with those from MEGASTROKE (Malik et al. 2018) and the UK Biobank hypertension GWAS results from OpenGWAS used by Zheng et al. (2023) were replaced with those from Pan-UKBB due to licensing restrictions. The GWAS of coronary artery calcification was not available either publicly or via application at the time of this analysis (Kavousi et al. 2022).↩︎