Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Exploring Potential Causal Genes for Immunoglobulin A Nephropathy: A Summary Data-Based Mendelian Randomization and FUMA Analysis

Version 1 : Received: 18 May 2022 / Approved: 20 May 2022 / Online: 20 May 2022 (12:13:06 CEST)

How to cite: Zhang, Q.; Zhang, K.; Zhu, Y.; Yang, J.; Zhang, M. Exploring Potential Causal Genes for Immunoglobulin A Nephropathy: A Summary Data-Based Mendelian Randomization and FUMA Analysis. Preprints 2022, 2022050277 (doi: 10.20944/preprints202205.0277.v1). Zhang, Q.; Zhang, K.; Zhu, Y.; Yang, J.; Zhang, M. Exploring Potential Causal Genes for Immunoglobulin A Nephropathy: A Summary Data-Based Mendelian Randomization and FUMA Analysis. Preprints 2022, 2022050277 (doi: 10.20944/preprints202205.0277.v1).

Abstract

Background: Immunoglobulin A nephropathy (IgAN) is a complex autoimmune disease, and the exact pathogenesis remains to be elucidated. Methods: We conducted summary data-based Mendelian randomization (SMR) analysis and performed functional mapping and annotation using FUMA to explore genetic loci that are po-tentially involved in the pathogenies of IgAN. Both analyses used summarized data of a recent genome-wide association study (GWAS) on IgANs, which included 477,784 Europeans (15,587 cases and 462,197 controls) and 175,359 East Asians (71 cases and 175,288 controls). We performed separate SMR analysis using CAGE and GTEx eQTL data. Results: Using the CAGE eQTL data, our SMR analysis identified 32 probes tagging 25 unique genes that were pleiotropically/potentially causally associated with IgAN, with the top three probes being ILMN_2150787 (tagging HLA-C, PSMR=2.10×10-18), ILMN_1682717 (tagging IER3, PSMR=1.07×10-16) and ILMN_1661439 (tagging FLOT1, PSMR=1.16×10-14). Using GTEx eQTL data, our SMR analysis identified 24 probes tagging 24 unique genes, with the top three probes being ENSG00000271581.1 (tagging XXbac-BPG248L24.12, PSMR=1.44×10-10), ENSG00000186470.9 (tagging BTN3A2, PSMR=2.28×10-10), and ENSG00000224389.4 (tagging C4B, PSMR=1.23×10-9). FUMA analysis identified 3 independent, significant and lead SNPs, 2 genomic risk loci and 39 genes. Conclusion: We identified many genetic variants/loci that are potentially involved in the patho-genesis of IgAN.

Keywords

immunoglobulin A nephropathy; expression quantitative trait loci; summary data-based Mendelian randomization; genome-wide association study; functional mapping

Subject

LIFE SCIENCES, Genetics

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