IMPROVING THROUGHPUT OF LONG READS WITH HIGH CONSENSUS BASE ACCURACY TO RESOLVE REPETITIVE DNAS

以高共识基础精度提高长读取的吞吐量，解决重复的 DNAS

• 批准号: 9920185
• 负责人: Karen Hayden Miga
• 金额: $ 30.6万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-23 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9920185
• 关键词: Alleles; Base Sequence; Benchmarking; Biomedical Research; CRISPR/Cas technology; Cell Line; Centromere; Chromosome Structures; Chromosomes; Complex; Consensus; DNA; DNA Modification Process; Data; Data Set; Diploidy; Disease; Genetic Variation; Genetic study; Genome; Genome Stability; Genomics; Goals; Health; High-Throughput Nucleotide Sequencing; Human; Human Chromosomes; Human Genome; Immunoglobulin Variable Region; Individual; Institutes; Length; Maps; Methods; Mutation; Phase; Platinum; RNA; Repetitive Sequence; Research; Resolution; Resources; Source; Structure; Technology; Testing; Utah; Variant; Work; X Chromosome; X Inactivation; arm; base; cohort; cost effective; design; genetic pedigree; human reference genome; improved; method development; nanopore; novel; novel strategies; organizational structure; reference genome; sequencing platform; telomere; tool

Project Summary/Abstract Approaches to complete the human genome will benefit from careful, benchmarked advances that demonstrate the capability to fully assemble and phase diploid chromosomes. The remaining unresolved regions in our high-resolution genomic maps are known to contain long tracts of repeats. The long-term objective of our research is to develop new experimental methods to complete chromosome scale assemblies to study the sequence organization, structural diversity, and disease impact of these novel sequences. The goal of this proposal is to develop sequencing methods to improve the sequence throughput of reads that are hundreds of kilobases in length to improve consensus base accuracy, a necessary step to advance assembly efforts into the remaining gapped regions. In our first aim, we demonstrate the use of our approach to generate the first telomere-to-telomere phased assembly of a human chromosome. We hypothesize that this work will be critical to complete other chromosome reference assemblies. In our second aim we present a new approach to target and enrich for long-reads in repetitive DNAs that were previously misrepresented or missing completely in previous reference assemblies. This approach is expected to provide a new cost-effective method of studying genetic variation in these highly variable regions from a large number of individuals. This research has the additional benefit that it will add new sequence to the human genome to systematically explore genetic variation of regions frequently overlooked as part of disease-association studies.

项目概要/摘要 完成人类基因组的方法将受益于仔细的、基准化的进展 证明了完全组装和定相二倍体染色体的能力。这 已知我们的高分辨率基因组图中剩余的未解析区域包含长 大片的重复。我们研究的长期目标是开发新的实验 完成染色体规模组装以研究序列组织的方法， 这些新序列的结构多样性和疾病影响。该提案的目标是 开发测序方法以提高数百个读数的序列吞吐量 千碱基长度以提高共识碱基准确性，这是推进的必要步骤 集会努力进入剩余的差距区域。在我们的第一个目标中，我们演示了使用 我们的方法产生人类第一个端粒到端粒的分阶段组装 染色体。我们假设这项工作对于完成其他染色体至关重要 参考组件。在我们的第二个目标中，我们提出了一种新的方法来瞄准和丰富 重复 DNA 中的长读段以前被错误表述或完全缺失 以前的参考组件。这种方法有望提供一种新的具有成本效益的方法 从大量数据中研究这些高度可变区域的遗传变异的方法 个人。这项研究还有一个额外的好处，那就是它将为人类添加新的序列 基因组系统地探索经常被忽视的区域的遗传变异 疾病关联研究。