Whole-exome and Whole-genome Sequencing of 1097 Individuals with Type 1 Diabetes Reveals Novel Genes for Diabetic Kidney Disease

Background and hypothesis Diabetic kidney disease (DKD) is a severe diabetic complication affecting one third of individuals with type 1 diabetes. Although several genes and common variants have been associated with DKD, much of the predicted inheritance remain unexplained. Here, we performed next-generation sequencing to assess whether low-frequency variants — single or aggregated — contribute to the missing heritability in DKD. Methods We performed whole-exome sequencing (WES) of 498 individuals and whole-genome sequencing (WGS) of 599 individuals with type 1 diabetes. After quality control, we had next-generation sequencing data available for altogether 1064 individuals, of whom 546 had developed either severe albuminuria or end-stage kidney disease, and 528 had retained normal albumin excretion despite a long duration of type 1 diabetes. Single variants and gene aggregate tests were performed separately for WES and WGS data and combined with meta-analysis. Furthermore, we performed genome-wide aggregate analyses on genomic windows (sliding-window), promoters, and enhancers with the WGS data set. Results In single variant meta-analysis, no variant reached genome-wide significance, but a suggestively associated THAP7 rs369250 variant ( P =1.50×10-5) was replicated in the FinnGen general population GWAS data for chronic kidney disease (CKD) and DKD phenotypes. Gene-aggregate meta-analysis identified suggestive evidence ( P <4.0×10-4) at four genes for DKD, of which NAT16 and LTA (TNB-β) replicated in FinnGen. Of the intergenic regions suggestively associated with DKD, the enhancer on chromosome 18q12.3 ( P =3.94×10-5) showed interaction with the METTL4 gene; the lead variant was replicated, and predicted to alter Mafb binding. Conclusions Our sequencing-based meta-analysis revealed multiple genes, variants and regulatory regions suggestively associated with DKD. However, as no variant or gene reached genome-wide significance, further studies are needed to validate the findings. What was known This study adds Potential impact ### Competing Interest Statement P-HG has served on advisory boards for AbbVie, Astellas, AstraZeneca, Bayer, Boehringer Ingelheim, Eli Lilly, Janssen, Medscape, MSD, Mundipharma, Novartis, Novo Nordisk, Sanofi, and has received lecture honoraria from Astellas, AstraZeneca, Bayer, Boehringer Ingelheim, Eli Lilly, Elo Water, Medscape, MSD, Mundipharma, Novartis, Novo Nordisk and Sanofi. P-H G has also received investigator-initiated grants from Eli Lilly and Roche. ### Funding Statement This study was supported by funding from Folkhalsan Research Foundation, Wilhelm and Else Stockmann Foundation, Liv och Halsa Society, Munuaissatio, Helsinki University Hospital Research Funds (EVO TYH2018207), Academy of Finland (299200, and 316664), Novo Nordisk Foundation (NNF OC0013659, NNF23OC0082732), the Sigrid Juselius Foundation, and the Finnish Diabetes Research Foundation. ### 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: This study was performed in accordance with the Declaration of Helsinki. Ethics committee of the Helsinki and Uusimaa Hospital District (491/E5/2006, 238/13/03/00/2015, and HUS-3313-2018) have given ethical approval for the study protocol, and all participants gave informed consent before participation. 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The FinnDiane WES and WGS datasets generated and/or analyzed during the current study are not publicly available as the participants’ written consent does not allow data sharing. The Readers may propose collaboration to research the individual level data with correspondence with the lead investigator.