A Table of all published GWAS with metabolomics

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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.

If you came this far, you may be interested in submitting your next paper to a Special Issue that I am currently guest-editing in MDPI Metabolites on “The Intersection of Metabolomics and Genomics and Their Role in Human Health” [CLICK HERE FOR MORE]

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 11 November 2021. 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].

BiofluidMetabolic traitsPlatformStudy population# TraitsCohort size# LociReference
SerumTargeted MSMS (Biocrates)German363 + all ratios2844Gieger et al., 2008
Plasma and SerumSphingolipidsMSEuropean33 + 43 ratios4,4005Hicks et al., 2009
SerumMainly phospholipidsMS (Biocrates)German, British163 + 26,406 ratios1,809 + 4229Illig et al., 2010
UrineNMR-derived metabolitesNMR (Chenomx)German59 + 1,661 ratios862 + 9925Suhre et al., 2011
Plasman-3 PUFAs (ALA, EPA, DPA, and DHA)Gas chromatographyEuropean ancestry (CHARGE)48,8663Lemaitre et al., 2011
SerumNon-targeted MS, knownsMS (Metabolon)German, British276 + 37 179 ratios1,768 + 1,05237Suhre et al., 2011
Urine and PlasmaUrine: NMR peaks, plasma: mainly phospholipidsNMR + MSBritishUrine: 512 peaks plasma: 163 + ratios2113Nicholson et al., 2011
SerumMainly lipid traitsNMR (Brainshake)Finnish117 + 99 ratios8,33031Kettunen et al., 2012
PlasmaPhospholipids + sphingolipidsMS (Biocrates)European1534,03435Demirkan et al., 2012
SerumMainly lipid traitsNMRFinnish117 + 99 ratios8,33030Tukiainen et al., 2012
SerumMainly lipid traits and low-weight metabolitesNMR (Brainshake)Finnish, British1301,905 + 4,70334Inouye et al., 2012
SerumNon-targeted MS, unknownsMS (Metabolon)German5171,76834Krumsiek et al., 2012
UrineNMR peaksNMRBrazil24252652Montoliu et al., 2013
PlasmaNMR peaksNMRGerman8,600 + 124,750 ratios1,7577Raffler et al., 2013
PlasmaFatty acids 16:0, 16:1n-7, 18:0, and 18:1n-9GC5 European cohorts4 8,9617Wu et al., 2013
SerumMS peaksMSSwedish6,138402 + 4897Hong et al., 2013
PlasmaAmino acids, amines, polar metabolites, lipidsMSUSA (European ancestry)2172,07631Rhee et al., 2013
UrineNMR peaksNMREuropean, Brazil1,276835 + 60111Rueedi et al., 2014
SerumNon-targeted MS, knowns and unknownsMSAfrican American3081,26019Yu et al., 2014
SerumNon-targeted MS, knowns and unknownsMS (Metabolon)European486 + 98,346 ratios7,824145Shin et al., 2014
SerumTargeted MS (mainly phospholipids) + non-targeted MS (knowns)MS (Metabolon & Biocrates)European344 (151 + 193)1,809 + 84312 newRied et al., 2014
SerumNMR-derived metabolitesNMREuropean422,1188Demirkan et al., 2015
SerumMainly phospholipidsMS (Biocrates)European1297,478 + 1,18231Draisma et al., 2015
BloodCirculating trans fatty acidsDiverse 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
UrineNMR-derived metabolites and NMR peaksNMREuropean15,379 features (incl. ratios) 3,861 + 1,69126Raffler et al., 2015
BloodAmino Acids and AcylcarnitinesMSEuropean962,10716Burkhardt et al., 2015
PlasmaFIA-MS derived, mainly acylcarnitines and amino acidsMSUS population631,490 + 2,0226Kraus et al., 2015
RBCFatty acids in RBCsGCFramingham Heart Study142,6335Tintle et al., 2015
BloodLipoprotein lipids and subclasses, fatty acids, amino acids, glycolysis precursorsNMR (Brainshake)14 cohorts from Europe12324,92562Kettunen et al., 2016
PlasmaNon-targeted MSLC-MSEuropean-American2172,076 + 1,5284Rhee et al., 2016
PlasmaNon-targeted MS focusing on carnitine pathways with whole genome sequencingLC-MSEuropean-American161,4562Yazdani et al., 2016
PlasmaNon-targeted MS with exome sequencingLC-MS (Metabolon)African-Americans3081,361 + 5084Yu et al., 2016
PlasmaCaffeine metabolitesUPLC- MS/MS or UPLC- ESI-MS/MSsix population-based studies of European ancestry4 + 1 ratio9,8764
Cornelius et al., 2016
Plasma + RBCs16:1n-7, 18:1n-7, 18:1n-9, 20:1n-9, 22:1n-9, 24:1n-9 fatty acidsgas chromatography or gas-liquid chromatographyMeta-analysis of Chinese and European ancestries63,521 + 12,02010Hu et al., 2017
PlasmaSmall peptide subset of the non-targeted Metabolon metabolomics platformMetabolon HD4European and African Americans (ARIC study)251,552 + 1,87222de Vries et al., 2017
PlasmaTargeted and Non-targeted MSBiocrates + MetabolonTwinsUK study160 + 4881,001 twins7Yet et al., 2016
PlasmaNon-targeted MSMetabolon HD4TwinsUK study6441,960 with three time points101
(17 genes with potential LoF variants)
Long et al., 2017
PlasmaNon-targeted MSMetabolon HD4Qatari826614 (exome seq) + 382 (2.5 Omni array)21 common + 12 rare variantsYousri et al., 2018
PlasmaAmino acidsNMRnon-diabetic
Finnish men
98,5455 common + 2 rare/gene-basedTeslovich et al., 2018
SerumNon-targeted MSLipid-related metabolites from Metabolon platformARIC1021552 European-and 1872 African-Americans, using WES and WGS7 novel lipid-related metabolite-genomic region associationsFeofanova et al., Genetics, 2018
PlasmaEicosanoids, endocannabinoids and sphingolipidsLC-MSBritish Caucasians175204 from 31 familiesN/AMcGurk et al., ASHG 2018 abstract
PlasmaAmino acids, acylcarnitines, sphingolipids MSSingapore Chinese162 + 70 ratios2,43417Chai et al., ASHG 2018 abstract
PlasmaNon-targeted MSMetabolon HD4INTERVAL and EPIC-Norfolk>900>14,000 + ~5,700488Surendran et al., ASHG 2018 abstract
PlasmaLipidomicsLipotype platformEuropean141 + 12 lipid classes2,04535 lipidspecies-
associated loci
Tabassum et al., Nature Comms, 2019, preprint BioRxiv, 2018 (presented at ASHG 2018)
Plasma + serumGlycineMetabolon HD4 + Biocrates p180 + NightingaleEuropean180,00327Wittemans et al., 2019
SerumNon-targeted MSMetabolon HD4Middle-aged individuals (45 to 64 years) from the ARIC study1221,37652 Loss of function variants (Exome sequencing, p<1E-6)Yazdani et al., 2019
NANANALIFE-Adult & LIFE-Heart studies8 steroid hormones7,66715 novelPott et al., J Clin Endocrinol Metab. 2019
PlasmaPlasma triglycerides, phospholipidsLC-MSLeiden Longevity Study, Netherlands Twin Register, Erasmus Rucphen Family (ERF) study90 lipids5,53734 replicated + 11 novelDemirkan et al., bioRxiv 2019
SerumNon-targeted MSMetabolon HD4 Elite athletes75149019 elite athlete mQTLs, 4 endurance mQTLsAl-Khelaifi et al., Scientific Reports, 2019
UrineNon-targeted MSMetabolon HD2/HD4Patients with reduced kidney function1,1721,627240Schlosser et al., Nature Genetics, 2020
SalivaNon-targeted MSMetabolon HD4 TwinsUK + SHIP4761,41914 metabolites at 11 lociAbhishek et al., Hum Mol Gen, 2020
SerumNon-targeted MSMetabolon HD4two cohorts (Israeli)1,17041368Bar et al., Nature, 2020
SerumPUFA, omega-3, omega-6, and LA and DHANMRPREDIMED Plus trial, Valencia, Spain54261 genome-wide sign. locus (FADS1 region) Coltell et al., Nutrients 2020
SerumNon-targeted MSMetabolon HD4Hispanic (Hispanic Community Health Study/Study of Latinos participants)6403,92646Feofanova et al., AJHG 2020
Cerebrospinal fluid (CSF)Non-targeted MSMetabolon HD4 WADRC and WRAP Alzheimer's studies33868916Panyard et al., Nature Comms, 2021, previously bioRxiv 2020
PlasmaNon-targeted MSin-house LC-MS/MS platform for polar lipophilic metabolitesFINRISK02 + replication in Framingham Heart Study11,067 features7,013 + 2,886118 loci associated with 2,319 featuresQin et al., medRxiv 2020
SerumDirect Infusion High-Resolution Mass Spectrometry (DIHRMS)in-house platform described herePakistan Risk of Myocardial Infarction Study (PROMIS) + British blood donors from the INTERVAL study340 lipid metabolites in PROMIS + 399 in INTERVAL5,662 in PROMIS + 13,814 in INTERVAL253 lipidQTLs at 24 independent loci in PROMIS + 502 lipid QTLs at 38 loci in INTERVALHarshfield et al., BMC Medicine 2021, preprint on medRxiv 2020
???TOPMed??Multi-Ethnic Whole-Genome Sequencing Analysis of Human Metabolome Identifies 93 Novel Genetic Loci Bing Yu et al., ASHG 2020
BloodMulti-platformBiocrates p180, Nightingale NMR, Metabolon HD4Fenland, EPIC-Norfolk, INTERVAL17486,507499 associations at 144 lociLotta et al., Nature Genetics, 2021, preprint
bioRxiv, 2020
PlasmaNon-targeted MSnot specified
Han Chinese161 + 12,280 ratios1,028 + 52313Wang et al., Clinical and Translational Medicine, 2021
UrineNon-targeted MSMetabolon HD4 German Chronic Kidney Disease (GCKD) cohort1487 + 53,714 ratios4,864 (4,795 for ratios)420 associations (MAF<1%), 38 gene associations for rare variant tests (60 for ratios)Cheng et al., Nature Communications, 2021
BloodTargeted & non-targeted MS (study also analyzed transciptomics & proteomics)Biocrates p150 & Metabolon HD2DIRECT study163 (Biocrates) + 223 (Metabolon)3,029301 independent metabolite-QTLsVinuela et al., medRxiv 2021
SerumNon-targeted MSMetabolon HD4African American Study of Kidney Disease and Hypertension652 61942Luo et al., Kidney Int., 2021
Urine1H NMRin-houseCaucasian1,276 features after QC55521Flitman et al., bioRxiv 2020
PlasmaUPLC–QTOFMSWest Coast Metabolomics Center at University of California DavisOld Order
Amish founder population
355 lipid species650five rare Amish enriched loci, three of which are novel, replicated 7 previously known common lociMontasser et al., bioRxiv 2021
PlasmaNon-targeted MSMetabolon HD4 Men from the late-settlement region of Finland, bottle-necked population1,3916,136 303 novel association signalsYin et al. (medRxiv 2021)
Plasma, mitochondrial DNATargeted MSBiocrates p150KORA study1512,718NA (mitochondrial DNA)Aboulmaouahib et al. (Human Molecular Genetics, 2021)