A Table of all published EWAS with deep molecular phenotypes (omics)

posted in: Resources

The number of genome-wide association studies (GWAS) with deep molecular phenotypes, especially metabolomics and proteomics, is rapidly increasing. On other places of this blog I maintain tables of published GWAS with metabolomics (mQTLs), proteomics (pQTLs), and DNA methylation (meQTLs).

Here I extend this collection by a table of all published epigenome-wide association studies (EWAS) with metabolomics, proteomics, and other deep molecular phenotypes. I include studies with a smaller set of traits (e.g. blood lipids) if they are of interest due to their large sample size and findings (i.e. reporting loci that overlap with multiomics traits).

Please read our review Connecting the epigenome, metabolome and proteome for a deeper understanding of disease (Suhre et al., J. Int. Medicine, 2021).

You may also be interested in the following resources:

Should you know of any study missing here, please let me know.

ReferenceStudy Population/CohortNumber of SamplesCpG-Trait AssociationsOmics Phenotype
Petersen et al. (Hum. Mol. Genet. 2014)German (KORA) population study181420 (excluding CpGs with genetic confounders)649 blood metabolic and lipid traits (Metabolon, Biocrates, and Numares/Lipofit platforms)
Orozco et al. (Cell Metabolism 2015)Mouse study90 inbred mouse strainsNAgenome-wide expression levels, proteomics, metabolomics, and 68 clinical traits (measured in liver)
Sayols-Baixeras (Hum. Molec. Genet., 2016)REGICOR study and Framingham Offspring Study (replication)645+2542 (replication)14 (9 genes + 2 intergenic loci)Lipid traits (total, low-density and high-density lipoprotein cholesterol, and triglycerides)
Braun et al. (Clin. Epigenet., 2017)Rotterdam Study725+760 (replication)5blood levels of triglycerides, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and total cholesterol
Nano et al. (Gastroenterology, 2017)Rotterdam Study731+719 (replication)8 (4 replicated)blood for liver enzyme levels, including gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST)
Ahsan et al. (PLoS Genet., 2017)Northern Sweden Population Health Study (NSPHS)between 698 and 1033124121 protein biomarkers (Proseek immuno-assay technology)
Wahl et al. (BBA, 2018)4 cohorts3000+7 (5 sites)IgG glycosylation (24 glycans measured by UPLC, 50 by LC/MS)
Orozco et al.. (Hum. Mol. Gen., 2018)Metabolic Syndrome in Men cohort20113 clinical traits at 21 loci32 clinical traits in subcutaneous abdominal adipose tissue
Huang et al. (Epigenomics, 2018)Emory Twin Study (ETS)180 male twinsNA12 annotated smoking-related metabolites identified from a metabolome-wide association study
Tindula et al. (Environmental Epigenetics, 2019) Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort81 mother-child pairs7 (after Bonferroni correction)92 metabolites measured by targeted metabolomics (SRM monitoring)
Hillary et al. (Nat. Comm., 2019)Lothian Birth Cohort 1936750 healthy older adults26 sites with the levels of 9 proteins92 protein levels from the Olink neurology panel
Huan et al. (Nat.Comm. 2019)Framingham Heart Study417092 putatively
causal CpGs for CVD traits by Mendelian randomization
CVD traits
Zaghlool et al. (Nat. Comm., 2020)German (KORA) population study and multi-ethnic QMDiab study944 + 344 (replication)98 (replicated)1123 blood circulating proteins (Somalogic aptamers)
Hillary et al. (Genome Medicine 2020), pre-print on BioRxivLothian Birth Cohort 1936876370 blood circulating protein levels (Olink inflammation panel)
Huan et al. (Epigenetics, 2020)Framingham Heart Study3565227 CpGs with 40 nearby miRNAs (cis-miR-eQTMs)283 blood circulating microRNAs (miRNA)
Battram et al., bioRxiv 2020Avon Longitudinal Study of Parents and Children (ALSPAC)940 (mothers)no Bonferroni sign. hit; 29 associations at P<1E-7400 “selected” ALSPAC traits (out of 2408), incl. Nightingale NMR data and body fat composition
Gomez‑Alonso et al. (Clinical Epigenetics, 2021)KORA, LOLIPOP, NFBC1966, and YFS cohorts5414161 associations, covering 16 CpG sites at 11 loci and 57 metabolic measures226 mostly lipid-related metabolic measures (NMR based)
Goodrich et al. (Epigenetics Insights 2021)Mother-child cohorts from 3 maternity hospitals in Mexico City (ELEMENT study)238 children (ages 8-14 years)76 with LINE-1 DNA methylation, 27 with HSD11B2, 103 with H19, and 4 with IGF23758 serum metabolite features (574 of which are
Yao et al. (Clinical Epigenetics, 2021)Framingham Heart Study, replication in KORA+InCHIANTI+BLSA4170 + 783 + 500 + 150 (replication)10% of 16,416 cis CpG-transcript pairs from
the discovery sample replicated
Gene expression, using Illumina & Affymetrix platforms
Jhun et al. (Nat. Comms., 2021)Meta-analysis of 15 EWASin Europeans, African Americans, and Hispanics16265148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectivelyBlood lipids (HDL, LDL, TG)
Nie et al. (J. Hazardous Materials, 2021)Non-smokers of the 2nd follow-up of the Wuhan-Zhuhai cohort212only CpGs associated with fasting glucose were reported (?)10 Polycyclic aromatic hydrocarbon (PAH) metabolites
Hillary et al. (Alzheimers Dement, 2022)Scottish Family Health Study 77826282 AD-associated proteins from the SOMAscan v4 affinity proteomics platform

(updated 3 January 2023)