Analysis of Patterns of Structural Variation in the 1000 Genomes Data Set

1000 个基因组数据集中的结构变异模式分析

• 批准号: 8129827
• 负责人: CHARLES LEE
• 金额: $ 84.9万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-18 至 2013-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8129827
• 关键词: Affect; Age; Architecture; Base Sequence; Biological; Cataloging; Catalogs; Categories; Cell physiology; Classification; Cloning; Code; Communities; Custom; DNA Sequence Rearrangement; DNA Transposable Elements; Data; Data Set; Databases; Elements; Event; Evolution; Family; Frequencies; Gene Proteins; Genes; Genetic Variation; Genome; Genomics; Genotype; Goals; Health; Human; Individual; Inheritance Patterns; Inherited; Length; Linkage Disequilibrium; Lymphocyte; Metabolic Pathway; Methodology; Methods; Minisatellite Repeats; Nature; Pattern; Phase; Play; Population; Population Genetics; Population Study; Principal Investigator; Production; Proteins; RNA Splicing; Recording of previous events; Relative (related person); Repetitive Sequence; Research; Role; Sequence Analysis; Signal Pathway; Single Nucleotide Polymorphism; Site; Structure; Transcript; Transcriptional Regulation; Untranslated Regions; Variant; Work; analytical method; base; computerized data processing; design; disease phenotype; genetic analysis; homologous recombination; interest; member; mutant; pressure; promoter; protein complex; research study; structural genomics; tool

DESCRIPTION (provided by applicant): The 1000 Genomes Project is an initiative to sequence the complete genomes of over 1000 individuals and create a reference set of common and uncommon genetic variation among various ethnic populations. This project aims to more comprehensively identify all types of genetic variation, including Single nucleotide polymorphisms (SNPs) and Structural genome variants (SVs) which include regions that have been duplicated, deleted, inverted, or translocated through the course of human evolution. Some of these structural variants have been correlated with many different disease phenotypes and thus play a major role in human health. In the course of the pilot phase of this project, numerous diverse, yet complementary, analytical methods have been developed to detect these types of variation on multiple sequencing platforms. Our research team includes members of the structural genomic variation analysis group for the 1000 genome project who have been conducting analysis from the 1000 genome project over the past year. We now propose to conduct a coordinated analysis of the complete SV dataset from the 1000 genome production project. Our common goal is to enhance the value of the thousand genomes project data by carrying out more detailed characterization of variants in terms (1) structure at the nucleotide sequence-level (2) functional impact on genes and proteins and (3) their distribution in human populations. Our work will take over where the data processing ends, and aim to make the complete 1000 genomes SV call set maximally useful to the biological community.

描述（由申请人提供）： 1000个基因组项目是一项主动性，旨在对超过1000个个体的完整基因组进行序列，并在各种种族种群之间创建一组常见和不常见的遗传变异。该项目的目的是更全面地确定所有类型的遗传变异，包括单核苷酸多态性（SNP）和结构性基因组变异（SV），其中包括通过人类进化过程重复，删除，倒置，倒置或翻译的区域。这些结构变体中的一些与许多不同的疾病表型相关，因此在人类健康中起着重要作用。在该项目的试点阶段的过程中，已经开发出了许多多样化但互补的分析方法来检测多个测序平台上的这些类型的变化。我们的研究团队包括1000个基因组项目的结构基因组变异分析组成员，他们在过去一年中一直从1000个基因组项目进行分析。现在，我们建议对1000个基因组生产项目的完整SV数据集进行协调分析。我们的共同目标是通过在核苷酸序列级别（1）对基因和蛋白质的功能影响以及（3）它们在人类种群中的分布进行更详细的变体表征来增强千基因组项目数据的价值。我们的工作将接管数据处理的范围，并旨在使完整的1000个基因组SV呼叫集对生物界最大程度地有用。

项目成果

forestSV: structural variant discovery through statistical learning.

• DOI: 10.1038/nmeth.2085
• 发表时间: 2012-07-01
• 期刊: NATURE METHODS
• 影响因子: 48
• 作者: Michaelson, Jacob J.;Sebat, Jonathan
• 通讯作者: Sebat, Jonathan

Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.

• DOI: 10.1016/j.cell.2012.11.019
• 发表时间: 2012-12-21
• 期刊: Cell
• 影响因子: 64.5
• 作者: Michaelson JJ;Shi Y;Gujral M;Zheng H;Malhotra D;Jin X;Jian M;Liu G;Greer D;Bhandari A;Wu W;Corominas R;Peoples A;Koren A;Gore A;Kang S;Lin GN;Estabillo J;Gadomski T;Singh B;Zhang K;Akshoomoff N;Corsello C;McCarroll S;Iakoucheva LM;Li Y;Wang J;Sebat J
• 通讯作者: Sebat J