Journal Article

Proteogenomic analysis integrated with electronic health records data reveals disease-associated variants in Black Americans

Barber, Jacob L., Wilson, James G., Wang, Thomas J., Sofer, Tamar, Katz, Daniel H., Rao, Prashant, Chen, Yii-Der Ida, Natarajan, Pradeep, Taylor, Kent D., Itan, Yuval, Ekunwe, Lynette, Chen, Zsu-Zsu, Raffield, Laura M., Deng, Shuliang, Robbins, Jeremy M., Liu, Yongmei, Durda, Peter, Johnson, W. Craig, Guo, Xiuqing, Hall, Michael E., Gerszten, Robert E., Farrell, Laurie, Benson, Mark D., Gillman, Madeline G., Rotter, Jerome I., Tracy, Russell P., Manichaikul, Ani W., Cruz, Daniel E., Tuftin, Bjoernar, Rich, Stephen S., Kars, Meltem Ece, Tahir, Usman A., Jain, Deepti, Reiner, Alex P.

2024

Overview

BACKGROUNDMost GWAS of plasma proteomics have focused on White individuals of European ancestry, limiting biological insight from other ancestry-enriched protein quantitative loci (pQTL).METHODSWe conducted a discovery GWAS of approximately 3,000 plasma proteins measured by the antibody-based Olink platform in 1,054 Black adults from the Jackson Heart Study (JHS) and validated our findings in the Multi-Ethnic Study of Atherosclerosis (MESA). The genetic architecture of identified pQTLs was further explored through fine mapping and admixture association analysis. Finally, using our pQTL findings, we performed a phenome-wide association study (PheWAS) across 2 large multiethnic electronic health record (EHR) systems in All of Us and BioMe.RESULTSWe identified 1,002 pQTLs for 925 protein assays. Fine mapping and admixture analyses suggested allelic heterogeneity of the plasma proteome across diverse populations. We identified associations for variants enriched in African ancestry, many in diseases that lack precise biomarkers, including cis-pQTLs for cathepsin L (CTSL) and Siglec-9, which were linked with sarcoidosis and non-Hodgkin's lymphoma, respectively. We found concordant associations across clinical diagnoses and laboratory measurements, elucidating disease pathways, including a cis-pQTL associated with circulating CD58, WBC count, and multiple sclerosis.CONCLUSIONSOur findings emphasize the value of leveraging diverse populations to enhance biological insights from proteomics GWAS, and we have made this resource readily available as an interactive web portal.FUNDINGNIH K08 HL161445-01A1; 5T32HL160522-03; HHSN268201600034I; HL133870.

• Publisher: American Society for Clinical Investigation
• Subject: Adult / African Americans / Aged / Analysis / Arteriosclerosis / Association analysis / Atherosclerosis / Biobanks / Biomes / Black or African American - genetics / Black people / Blood cell count / Blood proteins / Blood Proteins - genetics / Cathepsin L / CD58 antigen / Clinical Medicine / Disease / Disease susceptibility / Electronic Health Records / Electronic medical records / Electronic records / Eurocentrism / Female / Gene loci / Gene mapping / Genetic analysis / Genetic aspects / Genetic variation / Genetics / Genome-wide association studies / Genome-Wide Association Study / Genomes / Health aspects / Humans / Immunology / Lymphomas / Male / Medical records / Medical research / Medicine, Experimental / Methods / Middle Aged / Multiple sclerosis / Non-Hodgkin's lymphoma / Peptide mapping / Plasma / Plasma proteins / Proteins / Proteogenomics - methods / Proteomes / Proteomics / Quantitative Trait Loci / Sarcoidosis / Statistics