Northwest Genomics Center

西北基因组中心

• 批准号: 7853779
• 负责人: PHILIP P GREEN
• 金额: $ 1100.81万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7853779
• 关键词: Address; Affect; Algorithms; Amino Acid Sequence; Area; Biological Assay; Blood; Budgets; Candidate Disease Gene; Code; Complement; Complex; Computer software; Copy Number Polymorphism; Custom; DNA; DNA Resequencing; DNA Sequence; Data; Data Quality; Data Set; Deposition; Disease; Drops; Functional RNA; Funding; Generations; Genes; Genetic; Genetic Variation; Genome; Genomics; Genotype; Goals; Heart; Hematological Disease; Human; Human Genome; Image; Image Analysis; Individual; Lung; Methods; Mission; Molecular Profiling; National Heart, Lung, and Blood Institute; Open Reading Frames; Peptide Sequence Determination; Phenotype; Population Genetics; Production; Proteins; Protocols documentation; Quality Control; Reading; Relative (related person); Reporting; Research; Research Personnel; Resources; Sample Size; Sampling; Statistical Methods; Structure; Technology; Testing; Time; Variant; Vendor; Work; abstracting; base; cohort; cost; cost effective; database of Genotypes and Phenotypes; design; exome; genetic analysis; genome sequencing; genome-wide; genotyping technology; innovation; insertion/deletion mutation; instrument; interest; novel; novel strategies; programs; public health relevance; success; technology development; trait

DESCRIPTION (provided by applicant): Project Abstract: This application addresses the NHLBI-RFA-OD-09-004 for Large-scale DNA Sequencing and Molecular Profiling of Well-phenotyped NHLBI Cohorts. We propose to establish a sequencing center to perform the production-level resequencing of exomes from 10,000 genomic DNA samples derived from well-phenotyped NHLBI cohorts. Second generation methods for targeted capture and DNA sequencing have matured rapidly. Exome sequencing currently has advantages over whole genome sequencing for studies aimed at understanding the contribution of rare variants to heart, lung and blood diseases. These advantages include much lower costs per sample and an increased likelihood of identifying variants of large effect that are amenable to functional interpretation. In our preliminary studies, we developed methods for targeted capture and second generation sequencing of protein-coding sequences at a genome-wide scale, i.e. the exome. We are consistently able to identify coding variants at 96% of targeted bases for 5% of the sequencing effort required for a whole genome. The result is high quality exomes, with a concordance to genotype calls of >99.75% and a false discovery rate for novel variants of <1%. We also show the power of exome sequencing for the direct identification of the causative gene for a monogenic disease. This proof-of-concept serves as a starting point for extending exome sequencing to study extreme and/or complex phenotypes of relevance to the NHLBI mission. Improvements that increase throughput or decrease costs while maintaining high data quality will be integrated into the exome production pipeline. Our recent innovations include a novel algorithm that nearly doubles the usable amount of sequence data that can be extracted from second generation sequencing image sets. The production focus of our team will be complemented by experts in high-throughput sequencing and genotyping, technology development (experimental and algorithmic), the statistical analysis of rare variation, population genetics, and copy number variation. Samples will be received from NHLBI cohorts and undergo extensive quality control prior to exome sequencing. Following sequencing, we will deliver a fully annotated set of coding variants for each individual. For the final deliverable, we will develop a custom genotyping chip for up to 50,000 high-impact, nonsynonymous variants to be assayed on a larger set of cohort samples (up to 50,000). We anticipate working closely with cohort investigators and the NHLBI to maximize the scientific value of these data and of this program. PUBLIC HEALTH RELEVANCE: Project Narrative: Well-phenotyped cohorts provide a key resource for studying the contribution of genetic variation to traits related to heart, lung or blood diseases. Applying targeted capture and massively parallel sequencing of all protein coding regions in the human genome (the exome) to well-phenotyped cohorts will help to delineate the contributions of both rare and common protein-altering variants to common diseases for the first time.

描述(由申请人提供)：项目摘要：本申请针对NHLBI-RFA-OD-09-004，用于对表型良好的NHLBI队列进行大规模DNA测序和分子图谱分析。我们建议建立一个测序中心，对来自表型良好的NHLBI队列的10,000个基因组DNA样本进行生产水平的外显子重新测序。第二代靶向捕获和DNA测序方法已经迅速成熟。外显子组测序目前比全基因组测序具有优势，用于旨在了解罕见变异对心、肺和血液疾病的贡献的研究。这些优势包括每个样本的成本低得多，以及识别出适合于功能解释的大影响变体的可能性增加。在我们的初步研究中，我们开发了在全基因组范围内对蛋白质编码序列进行定向捕获和第二代测序的方法，即外显子组。我们始终能够在96%的靶向碱基上识别编码变体，而整个基因组所需的测序工作只需5%。结果是高质量的外显子组，与&gt；99.75%的基因呼唤的一致性和&lt；1%的新变种的错误发现率。我们还展示了外显子组测序的力量，用于直接识别单基因疾病的致病基因。这一概念验证是扩大外显子组测序的起点，以研究与NHLBI任务相关的极端和/或复杂表型。在保持高数据质量的同时增加产量或降低成本的改进将被整合到Exome生产管道中。我们最近的创新包括一种新的算法，它可以使从第二代测序图像集提取的可用序列数据量几乎翻一番。我们团队的生产重点将得到高通量测序和基因分型、技术开发(实验和算法)、稀有变异的统计分析、种群遗传学和拷贝数变异方面的专家的补充。样本将从NHLBI队列中获得，并在外显子组测序之前接受广泛的质量控制。测序后，我们将为每个个体提供一组完全注释的编码变体。对于最终交付的产品，我们将开发一种定制的基因分型芯片，用于多达50,000个高影响、非同义变体，并在更大的队列样本集(最多50,000个)上进行分析。我们期待与队列调查人员和NHLBI密切合作，以最大限度地发挥这些数据和该计划的科学价值。 公共卫生相关性：项目叙述：表型良好的队列为研究基因变异对心脏、肺或血液疾病相关特征的贡献提供了关键资源。将人类基因组(外显子组)中所有蛋白质编码区的定向捕获和大规模并行测序应用于表型良好的队列，将有助于首次描绘罕见和常见的蛋白质变化变体对常见疾病的贡献。