Human Genetic Variation and Disease

人类遗传变异与疾病

• 批准号: 10646423
• 负责人: Lynn Jorde
• 金额: $ 58.3万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-22 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10646423
• 关键词: Adult; Age; Amyotrophic Lateral Sclerosis; Blood; Blood specimen; Chronic Childhood Arthritis; Collection; DNA; DNA Insertion Elements; DNA Repair; DNA Repair Gene; Data; Detection; Disease; Event; Family; Funding; Generations; Genes; Genetic Diseases; Genetic Variation; Genome; Germ-Line Mutation; Human; Human Genetics; In Vitro; Longevity; Longitudinal Studies; Measurement; Measures; Methods; Mosaicism; Mutation; Participant; Pattern; Phenotype; Population Database; Premature Menopause; RNA Sequences; Resources; Sampling; Sequence Analysis; Somatic Mutation; System; Testing; Time; Utah; Variant; Whole Blood; Work; analytical tool; de novo mutation; genetic information; genetic pedigree; improved; in vivo; member; public repository; transcriptome sequencing; transmission process; whole genome

In this renewal, we will continue our studies of the causes and disease consequences of human genetic variation. We have generated whole-genome sequence (WGS) data from the three-generation Utah CEPH pedigrees to longitudinally characterize rates and patterns of de novo mutations (DNMs). We showed significant differences in the rates of accumulation of mutations among families, and we demonstrated that 10% of apparent DNMs are actually postzygotic events that result in mosaicism. We also showed that a higher rate of age-adjusted germline DNM transmission is significantly associated with a shorter lifespan and earlier menopause. These results imply that one’s germline DNM rate, which increases with age, is associated with the somatic mutation rate. In the next funding period, we will test this hypothesis directly using blood-derived DNA samples collected at three different time points in the same CEPH pedigree members over a 35-year time period. To our knowledge, this is the first long-term longitudinal study of germline and somatic mutation rates in human pedigrees. We also hypothesize that DNA repair mechanisms influence variation in both germline and somatic mutation rates. We will test this hypothesis using whole-genome sequence data (supported by separate funding) and RNA-seq data from freshly collected whole blood samples. We predict that lower expression of critical DNA repair genes will result in higher germline and somatic mutation rates. To increase our power to detect patterns and disease associations, we will (under separate funding) expand the CEPH pedigree collection to include more than 700 members of the fourth generation, who are now adults. We will also resample generations 2 and 3 for a third time. We will undertake WGS and RNA-seq in these study participants, creating a unique, publicly available repository of genetic information spanning four generations. More than 180 phenotypic measurements were made for generations 2 and 3 of the CEPH pedigrees 20 years ago, and the same measurements will be made for generation 4. These resources will allow us to explore the effects of genetic variation, including mutation rates and DNA repair, on a broad assortment of phenotypes across several generations. In addition, we will continue our work to develop new and improved methods for genome sequence analysis, including the detection of mobile element insertions. We will analyze WGS and RNA-seq data from members of large Utah disease pedigrees obtained from the Utah Population Database, focusing on amyotrophic lateral sclerosis and juvenile idiopathic arthritis. These projects involve analysis of WGS and RNA-seq data as well as functional analysis in in vitro and in vivo systems.

在这次更新中，我们将继续研究人类的病因和疾病后果 遗传变异。我们已经从三代人中产生了全基因组序列(WGS)数据 犹他州CEPH家系纵向描述从头突变(DNMs)的比率和模式。我们 在不同的家庭中，突变累积的速度有显著的差异，我们 研究表明，10%的表观DNM实际上是导致嵌合体的合子后事件。我们 还表明，年龄调整的生殖系DNM传播率较高与 寿命更短，更年期更早。这些结果表明，一个人的生殖系DNM率，即 随着年龄的增长，与体细胞突变率有关。在下一个资助期，我们将测试 这一假设直接使用了在三个不同的时间点收集的血液提取的DNA样本 在35年内拥有相同的CEPH血统成员。据我们所知，这是第一个长期的 人类家系生殖系和体细胞突变率的纵向研究。我们还假设 DNA修复机制影响胚系和体细胞突变率的变异。我们将测试 这一假设使用全基因组序列数据(由单独的资金支持)和rna-seq数据。 从新采集的全血样本中。我们预测关键DNA修复的低表达 基因将导致更高的生殖系和体细胞突变率。 为了增强我们检测模式和疾病关联的能力，我们将(在单独的 资金)扩大CEPH系谱收集，以包括第四个 一代人，他们现在是成年人。我们还将第三次对第二代和第三代进行重新采样。我们会 在这些研究参与者中进行WGS和RNA-SEQ，创建一个独特的、公开可用的存储库 跨越四代人的遗传信息。进行了180多项表型测量 对于20年前的第二代和第三代CEPH家系，将进行同样的测量 这些资源将使我们能够探索遗传变异的影响，包括突变 比率和DNA修复，在几代人的广泛的表型分类。 此外，我们将继续努力开发新的和改进的基因组检测方法。 序列分析，包括检测移动元件插入。我们将分析WGS和 犹他州人群中大型犹他病家系成员的RNA-SEQ数据 数据库，重点是肌萎缩侧索硬化症和青少年特发性关节炎。这些项目 包括WGS和RNA-SEQ数据的分析以及体外和体内系统的功能分析。

项目成果

Sensitivity of the polyDetect computational pipeline for phylogenetic analyses

• DOI: 10.1016/j.ab.2019.113516
• 发表时间: 2020-03-15
• 期刊: ANALYTICAL BIOCHEMISTRY
• 影响因子: 2.9
• 作者: Storer, Jessica M.;Walker, Jerilyn A.;Batzer, Mark A.
• 通讯作者: Batzer, Mark A.

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.

• DOI: 10.1186/s12859-018-2056-y
• 发表时间: 2018-02-20
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Flygare S;Hernandez EJ;Phan L;Moore B;Li M;Fejes A;Hu H;Eilbeck K;Huff C;Jorde L;G Reese M;Yandell M
• 通讯作者: Yandell M

Genetic Ancestry Testing: What Is It and Why Is It Important?

• DOI: 10.1001/jama.2020.0517
• 发表时间: 2020-03-17
• 期刊: JAMA
• 作者: Jorde LB;Bamshad MJ
• 通讯作者: Bamshad MJ

Association of West African ancestry and blood pressure control among African Americans taking antihypertensive medication in the Jackson Heart Study.

杰克逊心脏研究中服用抗高血压药物的非裔美国人的西非血统与血压控制关联。

• DOI: 10.1111/jch.13824
• 发表时间: 2020
• 期刊: Journal of clinical hypertension (Greenwich, Conn.)
• 作者: VanTassell,JonC;Shimbo,Daichi;Hess,Rachel;Kittles,Rick;Wilson,JamesG;Jorde,LynnB;Li,Man;Lange,LeslieA;Lange,EthanM;Muntner,Paul;Bress,AdamP
• 通讯作者: Bress,AdamP

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information.

• DOI: 10.1186/s12864-017-3767-6
• 发表时间: 2017-05-22
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Rustagi N;Zhou A;Watkins WS;Gedvilaite E;Wang S;Ramesh N;Muzny D;Gibbs RA;Jorde LB;Yu F;Xing J
• 通讯作者: Xing J