Whole Genome and Whole Exome Sequencing to Identify Genes for Type 2 Diabetes and Obesity

全基因组和全外显子组测序鉴定 2 型糖尿病和肥胖基因

• 批准号: 10253747
• 负责人: Leslie J Baier
• 金额: $ 99.73万
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10253747
• 关键词: Alleles; American Indians; Architecture; Asians; Candidate Disease Gene; Complex; D-Amino Acid Dehydrogenase; Data; Diabetic Nephropathy; Disease; Dopamine; Energy Metabolism; Ethnic group; European; Frequencies; Gene Frequency; Genes; Genomics; Genotype; Heritability; Hour; Human; In Vitro; Individual; Large-Scale Sequencing; Lead; Lipids; Methods; Minor; Modeling; Mutation; Non-Insulin-Dependent Diabetes Mellitus; Nonsense Codon; Obesity; Pathway interactions; Phase; Phenotype; Pima Indian; Plasma; Population; Prediabetes syndrome; Predisposition; Privatization; Proteins; Research Personnel; Role; Signal Transduction; Single Nucleotide Polymorphism; Sleep; Techniques; Variant; base; diabetes mellitus genetics; diabetes risk; disorder risk; exome; exome sequencing; genome sequencing; genome wide association study; genome-wide; insertion/deletion mutation; loss of function; new therapeutic target; novel; protein degradation; rare variant; trait; whole genome

American Indians have extremely high rates of T2D, diabetic nephropathy and obesity, yet large-scale sequencing efforts to identify disease loci have not included individuals from this ethnic group. Therefore, variants that are unique or enriched for in American Indians, which may identify new therapeutic targets for these diseases, remain largely unknown. To identify common variation that increases susceptibility to type 2 diabetes (T2D) and/or obesity, whole genome sequence data was generated on 335 Pima Indians. Sequencing was performed by Illumina (N=301) and Complete Genomics, Inc (N=34). 13 million variants were found, including 11 million SNPs, 1.6 million Indels and 255,802 substitutions. Among all SNPs, 2.7 million were novel. To obtain information on rare variants which could potentially have a large effect size on disease risk, we recently obtained whole exome sequence data on 8500 American Indians informative for type 2 diabetes, obesity, diabetic nephropathy and lipid levels . For the whole exome sequence data, approximately 1.7 million variants were detected in 8500 American Indians. Among these variants, 95% were single nucleotide polymorphisms and 5% were short insertions or deletions. Approximately 493,0000 of these variants occurred in at least 5 subjects, and these underwent single variant analysis for type 2 diabetes and BMI. In addition, gene based models(Burden and SKAT methods) were also employed. The exome sequencing showed that Pima Indians have a distinct allelic architecture compared to populations of European and East Asian ancestry. The Pima Indian exomes had many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private. We evaluated gene-burden associations of candidate genes for type 2 diabetes, BMI, and four major plasma lipids and found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. We also analyzed whole-exome sequence data in 373 healthy Pima Indians informative for 24-hour energy expenditure (24-h EE) since the identification of variants that influence energy metabolism may lead to new pathways to treat human obesity. We identified a variant which introduces a premature stop codon (Cys264Ter) in the DAO gene. This variant demonstrated the strongest association for 24-h EE, where the Ter allele associated with substantially lower 24-h EE (mean lower by 268 kcal/day) and sleeping EE (by 135 kcal/day). The Ter allele has a frequency=0.5% in Pima Indians, while is extremely rare in most other ethnic groups (frequency>0.01%). In vitro functional analysis showed reduced protein levels for the truncated form of DAO consistent with increased protein degradation. DAO encodes D-amino acid oxidase, which is involved in dopamine synthesis which might explain its role in modulating EE.

美国印第安人有极高的T2D、糖尿病肾病和肥胖症的比率，但大规模的疾病基因定位工作并没有包括这一种族的个体。因此，在美洲印第安人中独特或丰富的变异，可能识别这些疾病的新治疗靶点，在很大程度上仍不清楚。 为了确定增加2型糖尿病(T2D)和/或肥胖症易感性的常见变异，对335名皮马印第安人进行了全基因组序列数据的生成。测序由Illumina(N=301)和Complete Genology，Inc.(N=34)进行。发现了1300万个变异，其中包括1100万个SNPs，160万个Indels和255,802个替换。在所有SNP中，有270万个是新的。为了获得可能对疾病风险有很大影响的罕见变异的信息，我们最近获得了8500名美洲印第安人的完整外显子组序列数据，这些数据有助于了解2型糖尿病、肥胖症、糖尿病肾病和血脂水平。 在整个外显子组序列数据中，在8500名美洲印第安人中检测到大约170万个变异。在这些变异中，95%为单核苷酸多态，5%为短插入或缺失。大约493,0000个这些变异发生在至少5个受试者中，这些人接受了2型糖尿病和BMI的单一变异分析。此外，还采用了基于基因的模型(Burden和SKAT方法)。 外显子组测序表明，与欧洲和东亚血统的人群相比，皮马印第安人具有明显的等位基因结构。PIMA印度外显子有许多预测的功能丧失(PLOF)和高度丰富或私人的非同义变体。我们评估了2型糖尿病、体重指数和四种主要血脂候选基因的基因负担相关性，发现了11个基因的19个显著的基因负担关联，为优先考虑GWAS信号的候选效应基因提供了额外的证据。 我们还分析了373名健康皮马印第安人的全外显子组序列数据，这些数据为24小时能量消耗(24-hEE)提供了信息，因为识别影响能量代谢的变异可能会导致治疗人类肥胖的新途径。我们发现了一个在DAO基因中引入提前终止密码子(Cys264Ter)的变异体。该变异与24小时EE的相关性最强，其中Ter等位基因与显著较低的24小时EE(平均降低268千卡/天)和睡眠EE(降低135千卡/天)相关。Ter等位基因在皮马印第安人中的频率为0.5%，而在大多数其他种族中极其罕见(频率为0.01%)。体外功能分析显示，截短形式的DAO的蛋白质水平降低，与蛋白质降解增加一致。DAO编码D-氨基酸氧化酶，它参与多巴胺的合成，这可能解释了它在调节EE中的作用。