Identification of eight genomic protective alleles for mitochondrial diabetes by Kinship‐graph convolutional network

Author:

Wang Jiahao12,Yan Dandan3,Cui Haoyue4,Zhang Rong3,Ma Xiaojing3,Chen Luonan145,Hu Cheng36ORCID,Wu Jiarui145ORCID

Affiliation:

1. CAS Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China

2. College of Life Sciences University of Chinese Academy of Sciences Beijing China

3. Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Diabetes Institute Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China

4. School of Life Science and Technology ShanghaiTech University Shanghai China

5. Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou Zhejiang China

6. Institute for Metabolic Disease Fengxian Central Hospital Affiliated to Southern Medical University Shanghai China

Abstract

ABSTRACTAimsNearly 85% of maternally inherited diabetes and deafness (MIDD) are caused by the m.3243A>G mutation in the mitochondrial DNA. However, the clinical phenotypes of MIDD may also be influenced by the nuclear genome, this study aimed to investigate nuclear genome variants that influence clinical phenotypes associated with m.3243A>G mutation in MIDD based on whole‐genome sequencing of the patients belonging to pedigrees.Materials and MethodsWe analyzed a whole‐genome sequencing (WGS) dataset from blood samples of 38 MIDD patients with the m.3243A > G mutation belonging to 10 pedigrees, by developing a Kinship‐graph convolutional network approach, called Ki‐GCN, integrated with the conventional genome‐wide association study (GWAS) methods.ResultsWe identified eight protective alleles in the nuclear genome that have protective effects against the onset of MIDD, related deafness, and also type 2 diabetes. Based on these eight protective alleles, we constructed an effective logistic regression model to predict the early or late onset of MIDD patients.ConclusionsThere are protective alleles in the nuclear genome that are associated with the onset‐age of MIDD patients and might also provide protective effects on the deafness derived from MIDD patients.

Funder

National Natural Science Foundation of China

Publisher

Wiley

Subject

General Medicine,Endocrinology, Diabetes and Metabolism,Internal Medicine

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