Here you find references to all published mGWAS in humans, ordered by publication date. If a study is missing from this list, please let me know. Please note that I do not apply a strict inclusion criterion for what I would call a GWAS with metabolomics, or rather a GWAS with biochemical traits (such as a GWAS with cholesterol levels). The latter are well covered by the GWAS catalogue.
This table was initially published in Kastenmüller et al., Genetics of human metabolism: an update. Hum. Mol. Genet. 2015 and has been updated as of March 7, 2019 to include N=80k meta-analysis of glycine GWAS (not really a metabolomics GWAS, but given the fact that more metabolic traits are reported at the identified loci, and the sheer size of it makes in worth being reported here). If you are interested in associations at specific loci you may also use the SNiPA block annotation tool [read this post], and if you are looking for associations specific to certain metabolites, try the Metabolomics GWAS Server [read this post].
| Biofluid | Metabolic traits | Platform | Study population | # Traits | Cohort size | # Loci | Reference |
|---|---|---|---|---|---|---|---|
| Serum | Targeted MS | MS (Biocrates) | German | 363 + all ratios | 284 | 4 | Gieger et al., 2008 |
| Plasma and Serum | Sphingolipids | MS | European | 33 + 43 ratios | 4,400 | 5 | Hicks et al., 2009 |
| Serum | Mainly phospholipids | MS (Biocrates) | German, British | 163 + 26,406 ratios | 1,809 + 422 | 9 | Illig et al., 2010 |
| Urine | NMR-derived metabolites | NMR (Chenomx) | German | 59 + 1,661 ratios | 862 + 992 | 5 | Suhre et al., 2011 |
| Plasma | n-3 PUFAs (ALA, EPA, DPA, and DHA) | Gas chromatography | European ancestry (CHARGE) | 4 | 8,866 | 3 | Lemaitre et al., 2011 |
| Serum | Non-targeted MS, knowns | MS (Metabolon) | German, British | 276 + 37 179 ratios | 1,768 + 1,052 | 37 | Suhre et al., 2011 |
| Urine and Plasma | Urine: NMR peaks, plasma: mainly phospholipids | NMR + MS | British | Urine: 512 peaks plasma: 163 + ratios | 211 | 3 | Nicholson et al., 2011 |
| Serum | Mainly lipid traits | NMR (Brainshake) | Finnish | 117 + 99 ratios | 8,330 | 31 | Kettunen et al., 2012 |
| Plasma | Phospholipids + sphingolipids | MS (Biocrates) | European | 153 | 4,034 | 35 | Demirkan et al., 2012 |
| Serum | Mainly lipid traits | NMR | Finnish | 117 + 99 ratios | 8,330 | 30 | Tukiainen et al., 2012 |
| Serum | Mainly lipid traits and low-weight metabolites | NMR (Brainshake) | Finnish, British | 130 | 1,905 + 4,703 | 34 | Inouye et al., 2012 |
| Serum | Non-targeted MS, unknowns | MS (Metabolon) | German | 517 | 1,768 | 34 | Krumsiek et al., 2012 |
| Urine | NMR peaks | NMR | Brazil | 2425 | 265 | 2 | Montoliu et al., 2013 |
| Plasma | NMR peaks | NMR | German | 8,600 + 124,750 ratios | 1,757 | 7 | Raffler et al., 2013 |
| Plasma | Fatty acids 16:0, 16:1n-7, 18:0, and 18:1n-9 | GC | 5 European cohorts | 4 | 8,961 | 7 | Wu et al., 2013 |
| Serum | MS peaks | MS | Swedish | 6,138 | 402 + 489 | 7 | Hong et al., 2013 |
| Plasma | Amino acids, amines, polar metabolites, lipids | MS | USA (European ancestry) | 217 | 2,076 | 31 | Rhee et al., 2013 |
| Urine | NMR peaks | NMR | European, Brazil | 1,276 | 835 + 601 | 11 | Rueedi et al., 2014 |
| Serum | Non-targeted MS, knowns and unknowns | MS | African American | 308 | 1,260 | 19 | Yu et al., 2014 |
| Serum | Non-targeted MS, knowns and unknowns | MS (Metabolon) | European | 486 + 98,346 ratios | 7,824 | 145 | Shin et al., 2014 |
| Serum | Targeted MS (mainly phospholipids) + non-targeted MS (knowns) | MS (Metabolon & Biocrates) | European | 344 (151 + 193) | 1,809 + 843 | 12 new | Ried et al., 2014 |
| Serum | NMR-derived metabolites | NMR | European | 42 | 2,118 | 8 | Demirkan et al., 2015 |
| Serum | Mainly phospholipids | MS (Biocrates) | European | 129 | 7,478 + 1,182 | 31 | Draisma et al., 2015 |
| Blood | Circulating trans fatty acids | Diverse | 7 cohorts of European-ancestry, replication in 3 non-European cohorts | >5-7 (study dependent) | 8,013 + (1,082 + 669 + 657) | 1 (31 SNPs in FADS1/2 cluster) | Mozaffarian et al., 2015 |
| Urine | NMR-derived metabolites and NMR peaks | NMR | European | 15,379 features (incl. ratios) | 3,861 + 1,691 | 26 | Raffler et al., 2015 |
| Blood | Amino Acids and Acylcarnitines | MS | European | 96 | 2,107 | 16 | Burkhardt et al., 2015 |
| Plasma | FIA-MS derived, mainly acylcarnitines and amino acids | MS | US population | 63 | 1,490 + 2,022 | 6 | Kraus et al., 2015 |
| RBC | Fatty acids in RBCs | GC | Framingham Heart Study | 14 | 2,633 | 5 | Tintle et al., 2015 |
| Blood | Lipoprotein lipids and subclasses, fatty acids, amino acids, glycolysis precursors | NMR (Brainshake) | 14 cohorts from Europe | 123 | 24,925 | 62 | Kettunen et al., 2016 |
| Plasma | Non-targeted MS | LC-MS | European-American | 217 | 2,076 + 1,528 | 4 | Rhee et al., 2016 |
| Plasma | Non-targeted MS focusing on carnitine pathways with whole genome sequencing | LC-MS | European-American | 16 | 1,456 | 2 | Yazdani et al., 2016 |
| Plasma | Non-targeted MS with exome sequencing | LC-MS (Metabolon) | African-Americans | 308 | 1,361 + 508 | 4 | Yu et al., 2016 |
| Plasma | Caffeine metabolites | UPLC- MS/MS or UPLC- ESI-MS/MS | six population-based studies of European ancestry | 4 + 1 ratio | 9,876 | 4 | Cornelius et al., 2016 |
| Plasma + RBCs | 16:1n-7, 18:1n-7, 18:1n-9, 20:1n-9, 22:1n-9, 24:1n-9 fatty acids | gas chromatography or gas-liquid chromatography | Meta-analysis of Chinese and European ancestries | 6 | 3,521 + 12,020 | 10 | Hu et al., 2017 |
| Plasma | Small peptide subset of the non-targeted Metabolon metabolomics platform | Metabolon HD4 | European and African Americans (ARIC study) | 25 | 1,552 + 1,872 | 22 | de Vries et al., 2017 |
| Plasma | Targeted and Non-targeted MS | Biocrates + Metabolon | TwinsUK study | 160 + 488 | 1,001 twins | 7 | Yet et al., 2016 |
| Plasma | Non-targeted MS | Metabolon HD4 | TwinsUK study | 644 | 1,960 with three time points | 101 (17 genes with potential LoF variants) | Long et al., 2017 |
| Plasma | Non-targeted MS | Metabolon HD4 | Qatari | 826 | 614 (exome seq) + 382 (2.5 Omni array) | 21 common + 12 rare variants | Yousri et al., 2018 |
| Plasma | Amino acids | NMR | non-diabetic Finnish men | 9 | 8,545 | 5 common + 2 rare/gene-based | Teslovich et al., 2018 |
| Plasma | Eicosanoids, endocannabinoids and sphingolipids | LC-MS | British Caucasians | 175 | 204 from 31 families | N/A | McGurk et al., ASHG 2018 abstract |
| Plasma | Amino acids, acylcarnitines, sphingolipids | MS | Singapore Chinese | 162 + 70 ratios | 2,434 | 17 | Chai et al., ASHG 2018 abstract |
| Plasma | Seven biochemical classes | Multiple platforms (Biocrates p180, Nightingale, Metabolon HD4) | Fenland, INTERVAL, EPIC-Norfolk | 174 | 9,363 to 86,507 | 144 | Langenberg et al., ASHG 2018 abstract |
| Plasma | Non-targeted MS | Metabolon HD4 | INTERVAL and EPIC-Norfolk | >900 | >14,000 + ~5,700 | 488 | Surendran et al., ASHG 2018 abstract |
| Plasma | Lipidomics | Lipotype platform | European | 141 + 12 lipid classes | 2,045 | 35 | Tabassum et al., BioRxiv, 2018 (presented at ASHG 2018) |
| Plasma + serum | Glycine | Metabolon HD4 + Biocrates p180 + Nightingale | European | 1 | 80,003 | 27 | Wittemans et al., 2019 |
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