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Center for Human Reference Genome Diversity

人类参考基因组多样性中心

基本信息

批准号：
9905992
负责人：
Evan Eichler
金额：
$ 335.06万
依托单位：
UNIVERSITY OF CALIFORNIA SANTA CRUZ
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-18 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9905992
关键词：
Address Algorithms Attention Back Biology Blood specimen Budgets Callback Cell Line Centromere Chromosomes Code Collection Communities Complex Consent Country DNA Data Data Analyses Diploidy Disease Ensure Ethics Evaluation Feedback Fostering Foundations Future Gene Frequency Genetic Diseases Genetic Variation Genome Genomic medicine Genomics Goals Haploidy Haplotypes Health Human Human Genetics Human Genome Human Resources Individual Informatics Information Dissemination Informed Consent Institutes International Link Manuals Medical center Methods National Human Genome Research Institute New York Nucleotides Patients Persons Phase Population Production Protocols documentation Repetitive Sequence Research Research Personnel Resources Sample Size Sampling Structure Technology Third Generation Sequencing Time Validation Variant Work base biobank cloud platform cohort computerized data processing cost data sharing data warehouse genetic variant genome sequencing human reference genome lymphoblastoid cell line new technology novel outreach pan-genome prevent programs reference genome sample collection scaffold telomere vertebrate genome

项目摘要

Project Abstract The goal of our Center for Human Reference Genome Diversity is to generate as error-free, gapless, complete, and correctly haplotype-phased genome assemblies as possible from a set of 350 persons comprehensively capturing the full extent of human diversity. We aim to capture >99% of allelic variants with >1% allele frequency, and to provide these genomes as a resource to the international community to enable genomic medicine and research addressing fundamental unanswered questions in biology and disease. We will employ a multi-platform approach using cutting-edge long read and linked read technologies to obtain the highest quality phased genomes. Aim 1 will focus on sample collection and procuring cell lines from at least 350 individuals with a specific emphasis on filling in gaps in human diversity. Aim 2 will generate highly contiguous chromosomal level assemblies that are over 99% haplotype-phased for at least 700 haploid genomes from 350 diploid samples. Aim 3 will finish these genomes to be gapless from telomere-to-telomere (T2T) for each chromosome. Aim 4 will evaluate the genomes for accuracy and completeness and perform initial variant calling to assess the level of human diversity. We will use a novel combination of technologies, sequencing strategies, and algorithms that we and others developed to produce the highest quality and most complete genome assemblies to date. Our effort will specifically target regions that have been excluded by other efforts, including segmental duplications, centromeres, and acrocentric DNA. To achieve these aims we have assembled an exceptional team consisting of leaders from around the world in consent ethics, sample collection, sample extraction, and high-quality genome sequencing, assembly, finishing and evaluation. The team also has expertise in using genomic technologies to address a broad range of scientific questions, so is highly cognizant of the practical needs of biomedical researchers who will use this resource. The high-quality genomes produced will be passed to the Human Reference Genome Center (HGRC) and Genome Reference Representation (GRR) groups for curation and release. The result will be a pan-human genome reference, representing important human diversity not present in the current reference genome. The data we generate will enable a fundamental shift in human genetics, fostering new discoveries from the single-nucleotide to chromosomal levels and revealing a more accurate and global view of the human population.

项目摘要