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: 9356558
• 负责人: Shawn Edward Levy
• 金额: $ 473.76万
• 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 2019-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9356558
• 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.

项目摘要/摘要 扩展我们对先天缺陷和儿童癌的遗传贡献和病因的理解 将对受这些条件影响的人产生重大而直接的影响，并显着贡献 在成人条件下相关研究。此应用程序将创建Hudsonalpha-St裘德基因组 测序中心（HASJ-GSC）为生成提供高效且经验丰富的基因组资源 以及分析最多的小儿癌和出生的高质量序列和变异数据 缺陷在三年内与可用资金尽可能多的人群。我们在这里提出创新， Hasj-GSC的能力和经验，用于为Gabriella Miller儿童提供数据 可以访问并可用于研究社区并利用其最大影响的计划 未来几年。我们还提出了一个降低成本计划，以便可以测序的案件数量 每年支出的每一美元分析增加。 hasj-gsc将产生卓越质量的整体 所有样品的基因组序列和变异数据以及小儿癌样本，RNASEQ和全部 外显子数据。联合基因组，外显子和RNASEQ将为尽可能多的分辨率提供 了解小儿癌中观察到的遗传和功能基因组变化。 hasj-gsc Will 提供序列数据，分阶段的变体数据和结构性分娩的分阶段结构变体数据 Gabriella Kids First Program提供的缺陷样本和儿童癌症样品。 hasj- GSC还将提供可靠，高效的数据存储和数据访问能力，可提供快速，可靠的 以及项目/示例计划董事/本金的有效数据访问，共享和报告 研究人员（PDS/PIS）（X01 PDS/PIS）。最后，HASJ-GSC将支持有效提交序列 以及基因型和表型（DBGAP）的受控公共数据库以及其他数据 Gabriella Miller Kids First程序可能指定的数据库并与X01PDS/PIS协调 谁将将测序样品的表型数据提交给相同的数据库。