A Table of all published GWAS with proteomics

posted in: Resources

Here you find all published genome-wide association studies with multiplexed protein traits in blood (pGWAS). If a study is missing from this list, please let me know.

This table was initially published as Supplementary Table 1 in Suhre et al. (2017) (with 6 entries at the time). A much extended version can be found in our recent Nature Reviews Genetics paper “Genetics meets proteomics: perspectives for large population-based studies” (https://doi.org/10.1038/s41576-020-0268-2). The full paper can be read online using this link: https://t.co/DjWAknSqWq

As pGWAS expand, I also now include GWAS on other human body fluids and tissues (there are three pGWAS in CSF for now).

There are four pGWAS in human cell lines, which I keep here for the time being:

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 proteins, try the Proteomics GWAS Server  [read this post].

The Proteome PheWAS browser is a great tool to find out which proteins may be causal for certain diseases – using Mendelian Randomization [read the paper on BioRxiv].

Olink-improve – Genetics of the Cardiovascular Proteome is a web-server for pQTLs of the Olink platform.

ReferenceStudy population#Samples in study#Proteins assayed#pQTLs reportedPlatform type
Melzer et al. (PLoS Genet, 2008)Population study1200428Immuno-assay
Lourdusamy et al. (Hum Mol Genet, 2012)Elderly Europeans9677860Aptamer-based (SOMAscan v1)
Johansson et al. (PNAS, 2013)Two population cohorts10601635Mass-spectrometry
Kim et al. (PLoS One, 2013)Altzheimer's disease cohort52113228Immuno-assay
Orru et al. (Cell, 2013)Individuals from four clustered Sardinian villages162927223Immune traits (not really proteomics)
Stark et al. (PLoS Genetics, 2014)Yoruba HapMap lymphoblastoid cell lines68441NAMicro-western and reverse phase protein arrays
Enroth et al. (Nature Comm, 2014)Population study9707718Immuno-assay
Kauve et al., (PLoS Genet., 2014)CSF fluid from two Altzheimer's disease cohorts574595Immuno-assay for proteins relevant to Altzheimer's disease
Liu et al. (Mol Syst Biol, 2015)Female twins11334218Mass-spectrometry
Sun et al. (PLOS Genetics, 2016)Current and former smokers with and without COPD (SPIROMICS & COPDGene )134088527Multiplex immuno assays (Myriad-RBM)
Deming et al. (Sci Rep, 2016)Alzheimer cohort81814656Immuno-assay
Solomon et al. (Circ Cardiovasc Genet, 2016)Population study3305127Immuno-assay for proteins implicated in cardiovascular diseases
Ahola-Olli et al. (Am J Hum Genet, 2017)Population study82934827Immuno-assay for cytokines and growth factors
Di Narzo et al. (PLoS Genet, 2017)Inflammatory bowel disease (IBD) patients187112841Aptamer-based (SOMAscan 1.1k)
Suhre et al. (Nature Comm, 2017)KORA and QMDiab study (Germany and Qatar)13351124539Aptamer-based (SOMAscan 1.1k)
Sasayama et al. (Hum Mol Genet, 2017)CSF fluid from a Japanese population1331126476Aptamer-based (SOMAscan 1.1k)
Folkersen et al. (PLoS Genet., 2017)Population study33948379Immuno-assay for proteins implicated in cardiovascular diseases
de Vries et al. (Hum. Mol. Genet., 2017)1,552 European Americans and 1,872 African
Americans (ARIC study)
34242522Mass-spectrometry (small peptide subset of the non-targeted Metabolon metabolomics platform)
Ahsan et al. (PLoS Genet., 2017)Population study103312145Antibody-based proximity extension assay
Carayol et al. (Nature Comm, 2017)Obese subjects494112955Aptamer-based (SOMAscan 1.1k)
Benson et al. (Circulation, 2017)Framingham Heart Study and Malmö Diet and Cancer Study21801129161Aptamer-based, array based genotyping and exome seq
Patin et al. (Nature Immunology, 2018)unrelated, Western European ancestry, Milieu Intérieur cohort10008736Mean fluorescence intensity (MFI), cell surface marker (not really proteomics)
Sun et al. (Nature, 2018); pre-print on bioRxivInterval study (UK blood donors)330129941927Aptamer-based (SOMAscan in-house)
Emilsson et al. (Science, 2018)AGES Reykjavik study (Islanders over 65)5457 41373134Aptamer-based (SOMAscan in-house)
Yao et al. (Nature Comm, 2018); pre-print on bioRxivFramingham Heart Study 686171105Immuno-assay for proteins implicated in cardiovascular diseases, replication aptamer-based
Sliz et al. (J. Med. Genet., 2019), pre-print on bioRxivNorthern Finland Birth Cohort 1966 + meta-analysis in N=13,577 52841616Immuno-assay (Luminex / Milliplex, targeting chemokines & cytokines)
Mirauta et al. (BioRxiv, 2018)Human induced pluripotent stem cell lines (iPSC)202NA712Tandem Mass Tag Mass Spectrometry (TMT-MS)
Zhernakova et al. (Nature Gen. 2018)LifeLines Dutch population cohort126492214Immuno-assay (Olink CVD II panel)
Solomon et al. (Circulation: Genomic and Precision Medicine, 2018)Tromsø Study16566460Tandem mass tag mass spectrometry, with whole-exome sequencing
Zheng et al. (BioRxiv, 2019)A Mendelian Randomization study based on pGWAS (somewhat out of scope for this table, but VERY interesting)NA1002NAProteome PheWAS browser
Hillary et al. (Nat. Comm., 2019)Lothian Birth Cohort 19367509241Immuno-assay (Olink neurology panel)
Peters et al. (ASHG 2019 abstract)SCALLOP consortium1533592at least one pQTL for 71 out of 91 proteins; 12 had cis pQTLs only, 14 trans only, and 45 both cis and transImmuno-assay (Olink INF panel)
Wilson et al. (ASHG 2019 abstract)SCALLOP consortium1957818422,518 genome-wide significant SNPsImmuno-assay (Olink CVD II & III panels)
Klaric et al. (ASHG 2019 abstract)genetically isolated ORCADES cohort
105911023,545 pQTLs between 374 proteins and 968 genes mapping to
377 genomic regions
Immuno-assay (multiple Olink panels)
Yang et al. (ASHG 2019 abstract)CSF fluid, Alzheimer's disease, cases and controls52071382 proteins with cis-pQTLs, 20 proteins with novel trans-pQTLsProbably aptamer-based (SOMAscan 1.3k)
Robins et al. (bioRxiv, 2019) previously presented at ASHG 2019Dorsolateral prefrontal cortex (DLPFC) tissue from ROSMAP144 cognitively normal individuals7901 (tested in cis)28,221 pQTLs with 864 proteinsTandem mass tag (TMT) proteomics of brain tissue; uses Whole Genome Sequencing
Höglund et al. (Scientific Rep., 2019)Northern Swedish population health study (NSPHS)10057218 novelImmuno-assay (from Olink panels Oncology I and CVD I); uses Whole Genome Sequencing
Nath et al. (AJHG 2019)three population-based cohorts9267188 lociCytokines using multiplex fluorescent bead-based immunoassays
Folkersen et al. (Nature Metabolism, 2020), previous (BioRxiv, 2020) version, previously presented at ASHG 2019SCALLOP consortium, incl. 13 studies30,93190451 pQTLs for 85 proteinsImmuno-assay (Olink CVD-I panel)
Sjaarda et al. (AJHG, 2020)Latin Americans, ORIGIN study221623746 regions (not a GWAS, uses admixture mapping)Cardiometabolic biomarkers, Luminex 100/200 immunoassay platform
Gilly et al. (bioRxiv 2020)Hellenic Isolated Cohorts MANOLIS study1328257131Immuno-assay (Olink CVD-II, CVD-III, and MET panels), uses Whole Genome Sequencing
Emilsson et al. (bioRxiv 2020)AGES Reykjavik study (Islanders over 65)545747825553Aptamer-based (SOMAscan in-house)
Zhong et al. (BMC Genome Med, 2020)Longitudinal wellness cohort from Sweden101794144 pQTLs across 107 proteinsImmuno-assay (11 Olink panels)
Hillary et al. (Genome Medicine 2020), pre-print on BioRxivLothian Birth Cohort 19368767013Immuno-assay (Olink inflammation panel)
Ruffieu et al. (PLoS Comp Bio 2020), presented at ASHG 2018 abstract, pre-print on bioRxivOptifast Canadian cohort & DiOGenes cohort24331230136MS proteomics (130 proteins) and Aptamer-based (1100 proteins)
Bretherick et al. (PLoS Genetics, 2020)Isolated populations from the islands of Orkney (Scotland) and Vis (Croatia)up to 1992249 154Immuno-assay (Olink CVD2, CVD3, and INF panels)
Pietzner et al. (bioRxiv, 2020)Fenland study (UK)10,7084,775 proteins evaluated by 4,979 aptamers678 (regional sentinel pQTLs, reported in ST3)Aptamer-based (Somalogic V4 platform)
Zhang et al. (bioRxiv, 2021)Atherosclerosis Risk in Communities (ARIC) cohort study7,213 European Americans (EA) and 1,871 African Americans (AA)46651005 (AA) and 1384 (EA) cis-associations (trans not analyzed)Aptamer-based (Somalogic V4)
Venuela et al. (medRxiv 2021)DIRECT study3,0293731,592 cis-pQTLs, 533 trans-pQTLsImmuno-assay (four Olink panels: CVD I, II, II, Development & Metabolism); study also incl. metabolomics & transcriptomics GWAS