Related Experiment Video
Updated: Jun 4, 2025

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
A large-scale multi-omics polygenic risk score analysis identified candidate risk locus associated with rheumatoid
Jingni Hui1, Dan He1, Chen Liu1
1Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, 710061 Xi'an, China.
Objective:
This study aimed to investigate the associations of multi-omics polygenic risk score (PRS) and rheumatoid arthritis (RA) to identify potential genes/proteins and biological pathways.
Methods:
Based on multi-omics data from 48,813 participants in the INTERVAL cohort, we calculated multi-omics PRS for 13,646 mRNAs (RNASeq), 308 proteins (Olink), 2380 proteins (SomaScan), 726 metabolites (Metabolon), and 141 metabolites (Nightingale). Using the generalized linear model, we first evaluated the associations between multi-omics PRS and RA in 58,813 UK Biobank participants. The Gene Ontology (GO) project and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to identify the functional pathways in RA. Furthermore, differential gene expression profile datasets were used to validate the identified genes/proteins in our study.
Results:
We identified 59 transcriptomics PRS and 29 proteomics PRS significantly associated with RA. Both proteomics and transcriptomic PRS identified HLA-DQA2 (RNASeq: OR=1.19, P=1.18×10-24; SomaScan: OR=1.24, P=4.43×10-27) and AGER (RNASeq: OR=0.91, P=4.18×10-4; SomaScan: OR=0.93, P=3.97×10-3) were significantly associated with RA. Proteomic PRS from different profiling platforms (SomaScan and Olink) identified a consistent association between TFF3 (SomaScan: OR=0.90, P=4.08×10-6; Olink: OR=0.93, P=4.87×10-3) and RA. The identified gene/proteins were mainly enriched in the NF-kappa B signaling pathway (hsa04064, P=5.06×10-5) and Cytokine-cytokine receptor interaction (hsa04060, P=2.49×10-4). In addition, a total of 12 candidate genes in our study were verified in two independent GEO datasets, such as FLOT1 and ABCF1.
Conclusion:
Our findings provide novel insights into the involvement of identified genes/proteins and pathways in the pathogenesis of RA from multi-omics levels.
More Related Videos
08:27Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
08:51Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts
Published on: September 20, 2024
Related Concept Videos
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Pleiotropy
Polygenic Traits
Single Nucleotide Polymorphisms-SNPs
The JAK-STAT Signaling Pathway
Genomics