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.
| Reference | Study Population & Material | #Samples | #meQTLs | Comment |
|---|---|---|---|---|
| Zhang et al. (2010) | Human adult cerebellum samples | 153 | 12 trans-meQTLs, 736 cis-meQTLs | Illumina 27k array |
| Gibbs et al. (2010) | Four different tissues from 150 individuals: cerebellum, frontal cortex, caudal pons and temporal cortex | 600 | 490 trans-meQTLs, 2407 cis-meQTLs | Illumina 27k array, association data can be downloaded here |
| Bell et al. (2011) | Lymphoblastoid cell lines from 77 HapMap Yoruba individuals, | 77 | 180 cis-meQTLs, few trans | Illumina 27k array |
| Eijk et al. (2012) | Whole blood from healthy individuals of Dutch origin | 148 | 705 trans-meQTLs, 517 cis-meQTLs | Illumina 27k array |
| Drong et al. (2013) | Abdominal fat biopsies | 38 - replication in 181 females | 149 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 patients | 244 | 585 trans-meQTLs, 34,304 cis-QTLs | Illumina 450k array |
| Lemire et al. (2014) | Lymphocytes of 898 patients with colon cancer and 850 controls | 1748 | 1,919 trans-meQTLs | Illumina 450k array, 90% trans-meQTLs replicated in a separate study |
| Smith et al. (2014) | Tissue and blood from 7 study cohorts | 87 - 125, depending on cohort | 629 - 3049, depending on cohort | Illumina 27k array |
| Teh et al. (2014) | Umbilical cord samples from healthy babies (131 Chinese, 72 Malay, 34 Indian) | 237 | 1423 meQTLs (1037 with -logP>6.5) | Illumina 450k array |
| McClay et al. (2015) | Whole blood of a population cohort from Sweden | 697 | 683,152 cis-meQTLs, 819 distal cis-meQTLs, 286 trans-meQTLs out of 4,544,738 CpG sites | Methyl-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 age | cord 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 point | Illumina 450k array |
| Shakhbazov et al. (2016) | Whole blood from participants of the Brisbane Systems Genetics Study | 610 | 916 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 studies | 1714 | 25 schizophrenia associated meQTLs | Illumina 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) | 966 | 28 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 | 197 | NA | Illumina 450k array, query data set here |
| Zaghlool et al. (2016) | Whole blood from individuals of Arab ethnicity, including 18 elementary father-mother-child trios | 123 | 955 cis-meQTLs, with tri-modal distribution, showing Mendelian inheritance pattern | Illumina 450k array |
| Bonder et al. (2017) | Whole blood from multiple Dutch biobanks | 3841 | 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 5 | 10 cis-meQTLs that also influence cardio-vascular traits | Illumina 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) | 1980 | 2,025 trans-meQTLs (Bonferroni sign. & replicated) | Illumina 450k array, association data can be downloaded here |
| Hannon et al. (AJHG, 2018) | UK Household Longitudinal study | 1193 | 12,689,548 meQTLs between 2,907,234 genetic variants and 93,268 CpG sites | Illumina EPIC array (850k) |
| Huan et al. (Nature Comm, 2020) | Framingham Heart Study, replication in ARIC+GTP | 4170 + 1347 (replication) | 4.7 million cis- and 630 thousand trans-meQTL variants targeting >120 thousand CpGs | Illumina 450k array |
(updated August 8, 2020)
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