From genome to phenome via the proteome: broad capture, antibody-based proteomics to explore disease mechanisms

Studying the plasma proteome as the intermediate layer between the genome and the phenome has the potential to identify disease causing genes and proteins and to improve our understanding of the underlying mechanisms. Here, we conducted a cis -focused proteogenomic analysis of 2,923 plasma proteins measured in 1,180 individuals using novel antibody-based assays (Olink® Explore 1536 and Explore Expansion) to identify disease causing genes and proteins across the human phenome. We describe 1,553 distinct credible sets of protein quantitative trait loci (pQTL), of which 256 contained cis-pQTLs not previously reported. We identify 224 cis-pQTLs shared with 578 unique health outcomes using statistical colocalization, including, gastrin releasing peptide (GRP) as a potential therapeutic target for type 2 diabetes. We observed convergence of phenotypic consequences of cis-pQTLs and rare loss-of-function gene burden for twelve protein coding genes (e.g., TIMD4 and low-density lipoprotein metabolism), highlighting the complementary nature of both approaches for drug target prioritization. Proteogenomic evidence also improved causal gene assignment at 40% (n=192) of overlapping GWAS loci, including DKKL1 as the candidate causal gene for multiple sclerosis. Our findings demonstrate the ability of broad capture, high-throughput proteomic technologies to robustly identify new gene-protein-disease links, provide mechanistic insight, and add value to existing GWASs by enabling and refining causal gene assignment. ### Competing Interest Statement E.W. is now an employee of AstraZeneca. ### Funding Statement The EPIC-Norfolk study (DOI 10.22025/2019.10.105.00004) has received funding from the Medical Research Council (MR/N003284/1 MC-UU\_12015/1 and MC\_UU\_00006/1) and Cancer Research UK (C864/A14136). The genetics work in the EPIC-Norfolk study was funded by the Medical Research Council (MC\_PC\_13048).Proteomics measurements were supported by a collaboration agreement between the University of Cambridge and Olink. M.K. is supported by Gates Cambridge Trust. JCZS is supported by a 4-year Wellcome Trust PhD Studentship and the Cambridge Trust. C.L., E.W., M.P., N.K. and N.J.W. are funded by the Medical Research Council (MC\_UU_00006/1). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the Norfolk Research Ethics Committee (ref. 05/Q0101/191) and all participants gave their informed written consent before entering the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The EPIC-Norfolk data can be requested by bona fide researchers for specified scientific purposes via the study website (). Data will either be shared through an institutional data sharing agreement or arrangements will be made for analyses to be conducted remotely without the need for data transfer. Fine-mapped summary statistics for protein coding regions will be shared publicly following publication. Genome-wide association studies for anthropometric phenotypes have been conducted using the UK Biobank resource (application no. 44448). Access to the UK Biobank genotype and phenotype data is open to all approved health researchers ().