A Table of all published GWAS with metabolomics

posted in: Resources | 0

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 November 01, 2018 to include five mGWAS to be presented at ASHG 2018. 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
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
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
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
PlasmaSeven biochemical classesMultiple platforms (Biocrates p180, Nightingale, Metabolon HD4)Fenland, INTERVAL, EPIC-Norfolk1749,363 to 86,507144Langenberg 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 classes2,04535Tabassum et al., BioRxiv, 2018 (presented at ASHG 2018)