A Table of all published GWAS with DNA methylation

posted in: Resources

The number of association studies of DNA variation with CpG methylation – especially based on the Illumina 450k array – is steadily increasing. Quantitative trait loci for intermediate traits are particularly interesting to serve as instruments in Mendelian Randomization studies. On other places on this blog I maintain tables of published GWAS with metabolomics (mQTLs) and proteomics (pQTLs). Here you find a similar collection of studies that contain large numbers of DNA methylation QTLs (meQTLs). Should you know of any study missing here, please let me know.

ReferenceStudy Population & Material#Samples#meQTLsComment
Zhang et al. (2010)Human adult cerebellum samples15312 trans-meQTLs, 736 cis-meQTLsIllumina 27k array
Gibbs et al. (2010)Four different tissues from 150 individuals: cerebellum, frontal cortex, caudal pons and temporal cortex600490 trans-meQTLs, 2407 cis-meQTLsIllumina 27k array, association data can be downloaded here
Bell et al. (2011)Lymphoblastoid cell lines from 77 HapMap Yoruba individuals,77180 cis-meQTLs, few transIllumina 27k array
Eijk et al. (2012)Whole blood from healthy individuals of Dutch origin148705 trans-meQTLs, 517 cis-meQTLsIllumina 27k array
Drong et al. (2013)Abdominal fat biopsies38 - replication in 181 females149 using DMH, 5 meQTLs (out of 19 overlapping with 27k array) replicated Differential Methylation Hybridisation (DMH, Epigenomics AG, Germany), replication using Illumina 27k array
Shi et al. (2014)Histologically normal lung samples from non-small cell lung cancer patients244585 trans-meQTLs, 34,304 cis-QTLsIllumina 450k array
Lemire et al. (2014)Lymphocytes of 898 patients with colon cancer and 850 controls17481,919 trans-meQTLsIllumina 450k array, 90% trans-meQTLs replicated in a separate study
Smith et al. (2014)Tissue and blood from 7 study cohorts87 - 125, depending on cohort629 - 3049, depending on cohortIllumina 27k array
Teh et al. (2014)Umbilical cord samples from healthy babies (131 Chinese, 72
Malay, 34 Indian)
2371423 meQTLs (1037 with -logP>6.5)Illumina 450k array
McClay et al. (2015)Whole blood of a population cohort from Sweden697683,152 cis-meQTLs, 819 distal cis-meQTLs, 286 trans-meQTLs out of 4,544,738 CpG sitesMethyl-CpG binding domain (MBD) protein-based enrichment coupled to NGS (MBD-seq)
Gaunt et al. (Genome Biology, 2016)ARIES dataset: Samples taken at five different life stages in human blood: children at birth, childhood, adolescence and their mothers during pregnancy and middle agecord blood (771), childhood (834), adolescence (837), mothers during pregnancy (764), in middle age (742) between 24,262 and 31,729 sentinel associations at each time pointIllumina 450k array
Shakhbazov et al. (2016)Whole blood from participants of the Brisbane Systems Genetics Study610916 shared e/mSNPs and same chromosome probe pairs with a shared QTL(s)Illumina 450k array; see Suppl Tab 16 for association data
Hannon et al. (2016)Whole blood from three cohorts from schizophrenia studies171425 schizophrenia associated meQTLsIllumina 450k array, Hannon et al. (2017) provide links to meQTLs in blood and fetal brain
Hedman et al. (2016)Whole blood from men and women at age 70 living in Uppsala (Sweden)96628 oxidative-stress associated meQTLs Illumina 450k array, targeted analysis, no genome-wide meQTL scan
Chen et al. (2016)Three major human
immune cell types (CD14+ monocytes, CD16+ neutrophils,
and naive CD4+ T cells) from up to 197 individuals
197NAIllumina 450k array, query data set here
Zaghlool et al. (2016)Whole blood from individuals of Arab ethnicity, including 18 elementary father-mother-child trios123955 cis-meQTLs, with tri-modal distribution, showing Mendelian inheritance pattern Illumina 450k array
Bonder et al. (2017)Whole blood from multiple Dutch biobanks3841 10,141 trans-meQTLs at 1,907 different SNPs (FDR<0.05)Illumina 450k array, 90, all associations can be queried using the BIOS QTL browser
Richardson et al. (AJHG, 2017), (BioRxiv)Whole blood from 1,018 mother-offspring pairs (mothers at two timepoints and their offspring at three timepoints)1018 x 510 cis-meQTLs that also influence cardio-vascular traitsIllumina 450k array, association data can be obtained via MRbase, search for "data(aries_mqtl)"
McRae et al. (Scientific Reports2018), (BioRxiv)Whole blood from the Brisbane Systems Genetics Study (n=614 from 177 families) and the Lothian Birth Cohorts of 1921 and 1936 (combined n=1366)19802,025 trans-meQTLs (Bonferroni sign. & replicated)Illumina 450k array, association data can be downloaded here
Hannon et al. (AJHG, 2018) UK Household Longitudinal study119312,689,548 meQTLs between 2,907,234 genetic variants and 93,268 CpG sitesIllumina EPIC array (850k)
Huan et al. (Nature Comm, 2020)Framingham Heart Study, replication in ARIC+GTP4170 + 1347 (replication)4.7 million cis- and 630 thousand trans-meQTL variants targeting >120 thousand CpGsIllumina 450k array

(updated August 8, 2020)