Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes

识别和表征人类基因组中单倍型解析的结构变异的全谱

基本信息

  • 批准号:
    10190985
  • 负责人:
  • 金额:
    $ 269.6万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2013
  • 资助国家:
    美国
  • 起止时间:
    2013-09-20 至 2023-05-31
  • 项目状态:
    已结题

项目摘要

PROJECT SUMMARY The identification of structural variants (SVs) including deletions, insertions, duplications, and inversions from human whole-genome sequencing (WGS) data is essential for genomic research and precision medicine. However, SV discovery remains a challenge because no single sequencing technology or computer algorithm effectively captures the full spectrum of SVs. The Investigators of this project have made substantial advances toward comprehensive SV discovery by combining analyses from long- and short-read sequencing platforms, as well as incorporating other technologies such as jumping libraries, linked-read sequencing, and chromosomal strand-specific sequencing. Application of this approach to the genomes of three father-mother-child trios identified approximately threefold more SVs than could be detected using standard short-read WGS alone. This project builds on the Investigators’ ongoing work to develop optimized, integrated multi-technology computational pipelines for the comprehensive identification of SVs in human genomes. In Aim 1, computational methods will be developed for SV detection in WGS datasets generated using the multiple genomic technologies described above, and the combination of computational methods yielding the most comprehensive and accurate SV callset will be established as computational pipelines that will be packaged for broad sharing. This work will focus on family trios and unrelated individuals from all 26 populations of the 1000 Genomes Project. Use of trios will also enable determination of SV mutation rates for the different SV classes. Aim 2 will develop novel SV calling methods that address the challenging task of SV detection in short-read-only WGS datasets. This work will focus on genomes sequenced by large-scale NHGRI-funded initiatives that aim to identify genetic variants associated with disease, such as the Centers for Common Disease Genomics (CCDG) and Centers for Mendelian Genomics (CMG). Analyses of these short-read WGS datasets will yield a gold standard for genome-wide SV datasets and serve as a resource that can be used to genotype common variants across the larger number of CCDG, CMG, and other short-read WGS datasets. Execution of this project will generate deep coverage WGS and multi- technology genomic datasets, as well as new SV callsets, for individuals across 26 populations around the world. This data will be made widely available through an open FTP site. SV datasets for patient samples from CCDG and CMG will be accessible through dbGaP and enable a more comprehensive association of genetic variants with human diseases. All computational pipelines will be made available in a portable framework to promote wide adoption by other users. Overall, this project will establish SV reference sets spanning many human populations around the world in which all SVs (and small insertions and deletions) have been sequence resolved and correctly phased along the entire length of the chromosomes. This will serve as a valuable community resource for benchmarking SV discovery and genotyping across WGS datasets in the clinical and genomic research domains.
项目摘要 结构变异(SV)的鉴定,包括缺失、插入、重复和倒位, 人类全基因组测序(WGS)数据对于基因组研究和精准医学至关重要。 然而,SV的发现仍然是一个挑战,因为没有单一的测序技术或计算机算法, 有效地捕获SV的全部频谱。该项目的研究人员已经取得了实质性的进展 通过结合来自长读段和短读段测序平台的分析, 以及结合其他技术,如跳跃文库、连接阅读测序和染色体测序。 链特异性测序。该方法在三个父-母-子三人组基因组中的应用 鉴定了比单独使用标准短读WGS可检测到的SV多大约三倍的SV。这 该项目建立在调查人员正在进行的开发优化的,集成的多技术计算 用于全面鉴定人类基因组中的SV的管道。在目标1中,计算方法将 开发用于使用所描述的多种基因组技术生成的WGS数据集中的SV检测 以及计算方法的组合,产生最全面和准确的SV调用集 将被建立为计算管道,将被打包以供广泛共享。这项工作将侧重于 来自1000个基因组计划的所有26个群体的家庭三人组和无关个体。三人组的使用也将 能够确定不同SV类别的SV突变率。Aim 2将开发新的SV呼叫 解决在短只读WGS数据集中SV检测的挑战性任务的方法。这项工作将重点 由NHGRI资助的大规模计划对基因组进行测序,旨在识别与基因组相关的遗传变异。 常见疾病基因组学中心(CCDG)和孟德尔基因组学中心(Centers for Mendelian Genomics) (CMG)。对这些短读WGS数据集的分析将产生全基因组SV数据集的金标准, 作为一种资源,可用于对大量CCDG,CMG, 和其他短读WGS数据集。该项目的执行将产生深度覆盖的WGS和多- 技术基因组数据集,以及新的SV callsets,用于全球26个人群的个体。 这些数据将通过一个开放的FTP网站广泛提供。CCDG中患者样本的SV数据集 和CMG将通过dbGaP访问,并使遗传变异更全面的关联 人类疾病。所有计算管道都将在一个可移植的框架中提供,以促进 被其他用户广泛采用。总体而言,该项目将建立涵盖许多人类的SV参考集。 全世界所有SV(以及小的插入和缺失)都已得到序列解析的人群 并且沿着染色体的整个长度正确地定相沿着。这将成为一个有价值的社区 用于在临床和基因组研究中对WGS数据集的SV发现和基因分型进行基准测试的资源 研究领域。

项目成果

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Evan Eichler其他文献

Evan Eichler的其他文献

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{{ truncateString('Evan Eichler', 18)}}的其他基金

Diversity Action Plan: UW GenOM Project
多样性行动计划:华盛顿大学 GenOM 项目
  • 批准号:
    10189329
  • 财政年份:
    2020
  • 资助金额:
    $ 269.6万
  • 项目类别:
Center for Human Reference Genome Diversity
人类参考基因组多样性中心
  • 批准号:
    10686965
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
Center for Human Reference Genome Diversity
人类参考基因组多样性中心
  • 批准号:
    9905992
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
Center for Human Reference Genome Diversity
人类参考基因组多样性中心
  • 批准号:
    10020424
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
Center for Human Reference Genome Diversity
人类参考基因组多样性中心
  • 批准号:
    10269943
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
Center for Human Reference Genome Diversity
人类参考基因组多样性中心
  • 批准号:
    10488272
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
An "Embedded ELSI" Approach to the Creation of a Novel Human PanGenome Reference: Administrative Supplement to the Center for Human Reference Genome Diversity
创建新型人类泛基因组参考的“嵌入式 ELSI”方法:人类参考基因组多样性中心的行政补充
  • 批准号:
    10622227
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
ELSI Administrative Supplement - Center for Human Reference Genome Diversity
ELSI 行政补充 - 人类参考基因组多样性中心
  • 批准号:
    10423448
  • 财政年份:
    2019
  • 资助金额:
    $ 269.6万
  • 项目类别:
Sequence-resolved structural variation of human genomes
人类基因组的序列解析结构变异
  • 批准号:
    10202688
  • 财政年份:
    2018
  • 资助金额:
    $ 269.6万
  • 项目类别:
Northwest Genomics Center for All of Us
西北基因组学中心
  • 批准号:
    10884599
  • 财政年份:
    2018
  • 资助金额:
    $ 269.6万
  • 项目类别:

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