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.

Here are three older pGWAS in human cell lines, which I did not incorporate into the table:

And here a pGWAS conducted in mice:

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.

Reference#Samples in studyStudy population#Proteins assayed#pQTLs reportedPlatform type
Melzer et al. (PLoS Genet, 2008)1200Population study428Immuno-assay
Lourdusamy et al. (Hum Mol Genet, 2012)96Elderly Europeans77860Aptamer-based (SOMAscan v1)
Johansson et al. (PNAS, 2013)1060Two population cohorts1635Mass-spectrometry
Kim et al. (PLoS One, 2013)521Altzheimer's disease cohort13228Immuno-assay
Orru et al. (Cell, 2013)1629Individuals from four clustered Sardinian villages27223Immune traits (not really proteomics)
Stark et al. (PLoS Genetics, 2014)68Yoruba HapMap lymphoblastoid cell lines441NAMicro-western and reverse phase protein arrays
Enroth et al. (Nature Comm, 2014)970Population study7718Immuno-assay
Kauve et al., (PLoS Genet., 2014)574CSF fluid from two Altzheimer's disease cohorts595Immuno-assay for proteins relevant to Altzheimer's disease
Liu et al. (Mol Syst Biol, 2015)113Female twins34218Mass-spectrometry
Sun et al. (PLOS Genetics, 2016)1340Current and former smokers with and without COPD (SPIROMICS & COPDGene )88527Multiplex immuno assays (Myriad-RBM)
Deming et al. (Sci Rep, 2016)818Alzheimer cohort14656Immuno-assay
Solomon et al. (Circ Cardiovasc Genet, 2016)330Population study5127Immuno-assay for proteins implicated in cardiovascular diseases
Ahola-Olli et al. (Am J Hum Genet, 2017)8293Population study4827Immuno-assay for cytokines and growth factors
Di Narzo et al. (PLoS Genet, 2017)187Inflammatory bowel disease (IBD) patients112841Aptamer-based (SOMAscan 1.1k)
Suhre et al. (Nature Comm, 2017)1335KORA and QMDiab study (Germany and Qatar)1124539Aptamer-based (SOMAscan 1.1k)
Sasayama et al. (Hum Mol Genet, 2017)133CSF fluid from a Japanese population1126476Aptamer-based (SOMAscan 1.1k)
Folkersen et al. (PLoS Genet., 2017)3394Population study8379Immuno-assay for proteins implicated in cardiovascular diseases
de Vries et al. (Hum. Mol. Genet., 2017)34241,552 European Americans and 1,872 African
Americans (ARIC study)
2522Mass-spectrometry (small peptide subset of the non-targeted Metabolon metabolomics platform)
Ahsan et al. (PLoS Genet., 2017)1033Population study12145Antibody-based proximity extension assay
Carayol et al. (Nature Comm, 2017)494Obese subjects112955Aptamer-based (SOMAscan 1.1k)
Benson et al. (Circulation, 2017)2180Framingham Heart Study and Malmö Diet and Cancer Study1129161Aptamer-based, array based genotyping and exome seq
Patin et al. (Nature Immunology, 2018)1000unrelated, Western European ancestry, Milieu Intérieur cohort8736Mean fluorescence intensity (MFI), cell surface marker (not really proteomics)
Sun et al. (Nature, 2018); pre-print on bioRxiv3301Interval study (UK blood donors)29941927Aptamer-based (SOMAscan in-house)
Emilsson et al. (Science, 2018)5457AGES Reykjavik study (Islanders over 65) 41373134Aptamer-based (SOMAscan in-house)
Yao et al. (Nature Comm, 2018); pre-print on bioRxiv6861Framingham Heart Study 71105Immuno-assay for proteins implicated in cardiovascular diseases, replication aptamer-based
Sliz et al. (J. Med. Genet., 2019), pre-print on bioRxiv5284Northern Finland Birth Cohort 1966 + meta-analysis in N=13,577 1616Immuno-assay (Luminex / Milliplex, targeting chemokines & cytokines)
Mirauta et al. (eLife, 2020), preprint on BioRxiv, 2018202Human induced pluripotent stem cell lines (iPSC)NA712Tandem Mass Tag Mass Spectrometry (TMT-MS)
Zhernakova et al. (Nature Gen. 2018)1264LifeLines Dutch population cohort92214Immuno-assay (Olink CVD II panel)
Solomon et al. (Circulation: Genomic and Precision Medicine, 2018)165Tromsø Study66460Tandem mass tag mass spectrometry, with whole-exome sequencing
Zheng et al. (Nature Genetics, 2020), preprint on BioRxiv, 2019NAA Mendelian Randomization study based on pGWAS (somewhat out of scope for this table, but VERY interesting)1002NAProteome PheWAS browser
Hillary et al. (Nat. Comm., 2019)750Lothian Birth Cohort 19369241Immuno-assay (Olink neurology panel)
Peters et al. (ASHG 2019 abstract)15335SCALLOP consortium92at 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)19578SCALLOP consortium18422,518 genome-wide significant SNPsImmuno-assay (Olink CVD II & III panels)
Klaric et al. (ASHG 2019 abstract)1059genetically isolated ORCADES cohort
(Scotland)
11023,545 pQTLs between 374 proteins and 968 genes mapping to
377 genomic regions
Immuno-assay (multiple Olink panels)
Robins et al. (AJHG 2021), preprint on
bioRxiv, 2019
330Dorsolateral prefrontal cortex (DLPFC) tissue from ROSMAP73768,451 independent proximal brain pQTLs for 2,474 genes Tandem mass tag (TMT) proteomics of brain tissue; uses Whole Genome Sequencing
Höglund et al. (Scientific Rep., 2019)1005Northern Swedish population health study (NSPHS)7218 novelImmuno-assay (from Olink panels Oncology I and CVD I); uses Whole Genome Sequencing
Nath et al. (AJHG 2019)9267three population-based cohorts188 lociCytokines using multiplex fluorescent bead-based immunoassays
(Bio-Rad)
Folkersen et al. (Nature Metabolism, 2020), preprint on bioRxiv, 202030,931SCALLOP consortium, incl. 13 studies90451 pQTLs for 85 proteinsImmuno-assay (Olink CVD-I panel)
Sjaarda et al. (AJHG, 2020)2216Latin Americans, ORIGIN study23746 regions (not a GWAS, uses admixture mapping)Cardiometabolic biomarkers, Luminex 100/200 immunoassay platform
Gilly et al. (Nat. Comm. 2020), preprint on bioRxiv1328Hellenic Isolated Cohorts MANOLIS study257131Immuno-assay (Olink CVD-II, CVD-III, and MET panels), uses Whole Genome Sequencing
Emilsson et al. (bioRxiv 2020)5457AGES Reykjavik study (Islanders over 65)47825553Aptamer-based (SOMAscan in-house)
Zhong et al. (BMC Genome Med, 2020)101Longitudinal wellness cohort from Sweden794144 pQTLs across 107 proteinsImmuno-assay (11 Olink panels)
Dodig-Crnkovic et al. (EBioMedicine 2020)2,592 twinsSwedish Twin Registry (STR), participants born between 1911-195873415 cis-pQTLsAntibodies in suspension bead arrays
Hillary et al. (Genome Medicine 2020), pre-print on BioRxiv876Lothian Birth Cohort 19367013Immuno-assay (Olink inflammation panel)
Ruffieu et al. (PLoS Comp Bio 2020), pre-print on bioRxiv2433Optifast Canadian cohort & DiOGenes cohort1230136MS proteomics (130 proteins) and Aptamer-based (1100 proteins)
Bretherick et al. (PLoS Genetics, 2020)up to 1992Isolated populations from the islands of Orkney (Scotland) and Vis (Croatia)249 154Immuno-assay (Olink CVD2, CVD3, and INF panels)
Pietzner et al. (Nature Comm, 2021), preprint on
bioRxiv
10,708Fenland study (UK)4,775 proteins evaluated by 4,979 aptamers220 cis-pQTLs for 97 proteinsAptamer-based (Somalogic V4 platform)
Zhang et al. (Nature Genetics, 2022), preprint on
(bioRxiv)
7,213 European Americans (EA) and 1,871 African Americans (AA)Atherosclerosis Risk in Communities (ARIC) cohort study46571005 (AA) and 1384 (EA) cis-associations (trans not analyzed)Aptamer-based (Somalogic V4)
Venuela et al. (medRxiv 2021)3,029DIRECT study3731,592 cis-pQTLs, 533 trans-pQTLsImmuno-assay (four Olink panels: CVD I, II, II, Development & Metabolism); study also incl. metabolomics & transcriptomics GWAS
Zhong et al., (Nature Comm. 2021)101Longitudinal wellness cohort from Sweden1463331 associations between 143 proteins and 321 independent genetic variantsImmuno-assay (Olink Explorer platform)
Gurinovich et al. (GeroScience, 2021)224New England Centenarian Study (NECS)4131Supp Tab 3 provides pQTL data for 21 age-associated variants with 3641 aptamersAptamer-based (Somalogic V4? platform)
Gudjonsson et al. (Nat. Comm. 2022),
(bioRxiv 2021)
5368AGES study (Islanders over 65)47824113Aptamer-based (SOMAscan in-house)
Yang et al. (Nature Neuroscience, 2021), preprint medRxiv835, 529, and 380 CSF, plasma, and brain samples, resp.Three tissues (cerebrospinal fluid, plasma, brain) from Europeans with and without Alzheimer's disease713, 931, and 1079 proteins after QC in in CSF, plasma, and brain, resp.274, 127 and 32 pQTLs for CSF, plasma, and brain, resp.Aptamer-based (SOMAscan 1.3k)
Pietzner et al. (Science, 2021)12,084fasted EDTA-plasma samples from the Fenland study4,77510,674 pQTLs for 3,892 proteinsAptamer-based (Somalogic V4 platform)
Katz et al. (Circulation, 2021)1,852Black adults from the Jackson Heart Study1,301569Aptamer-based (SOMAscan 1.3k)
Ferkingstad et al. (Nature Genetics, 2021)35,559Icelanders4,90718,084Aptamer-based (Somalogic V4 platform)
Png et al. (Nat Comm, 2021)2,893MANOLIS and Pomak, part of the Hellenic Isolated Cohorts (HELIC)184214 pQTLs for 107 proteinsImmuno-assay (Olink neurology and neuro-exploratory panels)
Preprint on Research Square, 2022288postmortem human brain samples (179 males, 109 females) from the Stanley Medical Research Institute (SMRI) and Banner Sun Health Research Institute (BSHRI)11,672788 cis-pQTLs with 883 proteins 11-plex tandem mass tag (TMT) coupled with two-dimensional liquid chromatography-tandem mass spectrometry (LC/LC-MS/MS)
Sun et al., bioRxiv 20221,472UK Biobank, frequent variants with imputed genotype35,571 (discovery) and 18,181 (replication)10,248 primary associations across 2,928 independent genetic regionsOlink Explore 1536 platform
Katz et al., Science Advances 2022568 (Jackson Heart Study), 219 (HERITAGE Family Study)Jackson Heart Study and HERITAGE Family Study1301 (SomaScan1.3K), 4979 (SomaScan5K), 1472 (Olink Explore)
425 known + 373 new cis-pQTLsSomaScan1.3K, SomaScan5K, Olink Explore
Thareja et al., Human Mol. Genetics (in press) 2,935Qatar Biobank, whole genome sequencing1,3012,685SomaScan1.3k
He et al., BMC Biology, 2020287 normal human liver samples 1,508 900 local pQTL variants and 4026 distant pQTL variantsLC-MS/MS using DIA-TPA
Dhindsa et al. medRxiv 202250,829UK Biobank, rare variants with exome seq1,4723,674Olink Explore 1536 platform
Hou et al. (ASHG abstract, 2022)13,227UK Biobank European participants with WGS data1,4632,374Olink Explore 1536 platform
Chen et al. (ASHG abstract, 2022)1,002Women’s Health Initiative (WHI) 552not specifiedtargeted Olink panels
Koprulu et al. (ASHG abstract, 2022)1,180not specified 2,9231,553 cis-pQTLsa novel antibody-based assay (source not specified)
Richardson et al. (ASHG abstract, 2022)42,000UK Biobank Pharma Proteomics Project1,462not specifiedOlink Explore 1536 platform
Kuliesius et al. (ASHG abstract, 2022)not specifiedViking Health Study - Shetland6,434456Somalogic aptamer-based technology
Cruchaga et alk. (ASHG abstract, 2022)3,065Cerebrospinal fluid (CSF)7,5842,472Somalogic aptamer-based technology [study also has Metabolon mQTLs]
Cai et al. (ASHG abstract, 2022)1,537 AA, 883 EA,1062 EA from Framingham Heart StudyAfrican American (AA) and European American (EA) from the Women's Health Initiative1,4721,678 (AA), 1,153 (EA)Olink Explore 1536 platform
Siddiqui et al. (ASHG abstract, 2022)139Late-stage Alzheimer’s disease (case/control)5,060/4,706 from DDA/DIA73/59 cis-pQTLs and 1,527/3,288 trans-pQTLs from DDA/DIA Proteograph Product Suite (Seer Inc.) using nanoparticle-based enrichment, DIA and DDA MS/MS
Chiou et al. (ASHG abstract, 2022)35,306UK Biobank Pharma Proteomics Project1,424 28,867 Olink Explore 1536 platform
Sun et al. (ASHG abstract, 2022)-This study is already included here (see Sun et al., bioRxiv 2022)---
Wingo et al. (ASHG abstract, 2022)1,100Brain proteomes (dorsolateral prefrontal cortex), European ancestry 10,1981,171 SNP-by-sex interactionsnot specified
Surapaneni et al. (Kidney International, 2022)466Serum of African Americans6,790696SOMAScan 4.1
Hansson et al. (EMBO Mol. Med. 2022)1,591Cerebrospinal fluid (CSF)398176Olink panels (CVD-III, INF-I, NEU-I, NEUEXP) + other assays (ELISA, Meso Scale Discovery, ..)
Caron et al. (Genome Medicine, 2022)400Milieu Intérieur cohort, France229152Luminex
Hillary et al. (Alzheimers Dement, 2022)1,064Scottish Family Health Study 282 AD associated proteins64 SOMAscan v4
Koprulu et al. (Nature Metabolism, 2023)2,923EPIC-Norfolk (UK)1,180256 unreported pQTLsOlink Explore 1536 and Explore Expansion assays
Niu et al., medRxiv 20231,914HOLBAEK Study, children and adolescents (Denmark)420712 for 158 proteinsDIA-MS
Xu et al. (Nat. Comm., 2023)2,958Han Chinese304195SWATH-MS
Suhre et al. (bioRxiv 2023)52,705UK Biobank Pharma Proteomics Project2,821 ratios8,462 rQTLsOlink Explore 1536 platform