Characterizing pediatric genomes through an optimized sequencing approach

通过优化的测序方法表征儿科基因组

• 批准号: 9565172
• 负责人: Shawn Edward Levy
• 金额: $ 276.52万
• 依托单位: HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-23 至 2019-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9565172
• 关键词: Address; Adult; Affect; Child; Childhood; Clinical; Communicable Diseases; Communities; Congenital Abnormality; Data; Data Quality; Data Storage and Retrieval; Databases; Detection; Disease; Emotional; Etiology; Event; Family member; Funding; Gene Fusion; Generations; Genetic; Genetic Transcription; Genome; Genomics; Goals; Haplotypes; Healthcare; Heart Abnormalities; Infant Mortality; Investigation; Malignant Childhood Neoplasm; Malignant Neoplasms; Minority; Molecular; Molecular Analysis; Mutation; Operative Surgical Procedures; Parents; Pathway interactions; Pediatric Neoplasm; Pertussis; Phase; Phenotype; Physiological; Poliomyelitis; Prevention; Principal Investigator; Production; RNA; Reporting; Research; Research Personnel; Research Proposals; Resolution; Resources; Saint Jude Children' s Research Hospital; Sampling; Sequence Analysis; Societies; Structural Congenital Anomalies; Vaccination; Variant; base; cancer genome; cohort; cost; data access; data resource; database of Genotypes and Phenotypes; design; exome; exome sequencing; experience; functional genomics; genome sequencing; genome-wide; genome-wide analysis; genomic data; improved; innovation; leukemia; phenotypic data; prevent; proband; programs; therapeutic development; tool; transcriptome sequencing; tumor; tumor heterogeneity; whole genome

PROJECT SUMMARY/ABSTRACT Expanding our understanding of the genetic contributions and etiologies of birth defects and childhood cancer will have a significant and direct impact on those affected by those conditions and also contributes significantly to related research in adult conditions. This application will create the HudsonAlpha-St Jude Genome Sequencing Center (HASJ-GSC) to provide an efficient and experienced genomics resource for the generation and analysis of high quality sequence and variant data from the largest number of pediatric cancer and birth defect cohorts as possible with available funds over a three year period. We present here the innovation, capabilities, and experience of the HASJ-GSC to produce data for the Gabriella Miller Kids First Research Program that will be accessible and available to the research community and leveraged to its maximal impact for years to come. We also present a cost reduction plan so the number of cases that can be sequenced and analyzed per dollar spent increases each year. The HASJ-GSC will generate exceptional quality whole- genome sequence and variant data for all samples and for the pediatric cancer samples, RNASeq and whole- exome data. The combine genome, exome and RNASeq will provide as much resolution as possible to understanding the genetic and functional genomic changes observed in pediatric cancer. The HASJ-GSC will provide sequence data, phased variant data, and phased structural variant data from cohorts of structural birth defect samples and childhood cancer samples that the Gabriella Kids First Program will provide. The HASJ- GSC will also provide a reliable and efficient data storage and data access capability that provides fast, reliable and efficient data access, sharing and reporting for the project/sample Program Directors/Principal Investigators (PDs/PIs) (X01 PDs/PIs). Finally, the HASJ-GSC will support efficient submission of sequence and variant data to the controlled public database of Genotypes and Phenotypes (dbGaP), and other databases that may be designated by the Gabriella Miller Kids First Program and coordinate with X01PDs/PIs who will submit the phenotypic data of the sequenced samples to the same databases.

项目概要/摘要 扩大我们对出生缺陷和儿童癌症的遗传贡献和病因的理解 将对受这些情况影响的人产生重大和直接的影响，并且也做出重大贡献 成人条件下的相关研究。该应用程序将创建 HudsonAlpha-St Jude 基因组 测序中心（HASJ-GSC）为一代人提供高效且经验丰富的基因组学资源 对来自最大数量儿科癌症和出生的高质量序列和变异数据进行分析 在三年内利用可用资金尽可能地减少缺陷群体。我们在这里展示创新， HASJ-GSC 为 Gabriella Miller Kids First Research 生成数据的能力和经验 该计划将可供研究界访问和使用，并发挥其最大影响力 未来几年。我们还提出了一个降低成本的计划，以便可以排序的案例数量和 分析的每美元支出逐年增加。 HASJ-GSC 将产生卓越品质的整体 所有样本和儿科癌症样本、RNASeq 和整体的基因组序列和变异数据 外显子组数据。基因组、外显子组和 RNASeq 的结合将提供尽可能多的分辨率 了解在儿科癌症中观察到的遗传和功能基因组变化。 HASJ-GSC 将 提供来自结构出生队列的序列数据、阶段性变异数据和阶段性结构变异数据 加布里埃拉儿童优先计划将提供缺陷样本和儿童癌症样本。 HASJ- GSC还将提供可靠、高效的数据存储和数据访问能力，提供快速、可靠的数据存储和数据访问能力。 项目/样本项目总监/负责人的高效数据访问、共享和报告 研究人员 (PD/PI) (X01 PD/PI)。最后，HASJ-GSC 将支持序列的高效提交 和变异数据到受控的基因型和表型公共数据库 (dbGaP)，以及其他 可能由 Gabriella Miller Kids First 计划指定并与 X01PD/PI 协调的数据库 谁将把测序样本的表型数据提交到同一数据库。