Journal article
Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles
Nucleic acids research, Vol.52(5), pp.2212-2230
03/21/2024
DOI: 10.1093/nar/gkae086
PMID: 38364871
Abstract
Nonreference sequences (NRSs) are DNA sequences present in global populations but absent in the current human reference genome. However, the extent and functional significance of NRSs in the human genomes and populations remains unclear. Here, we de novo assembled 539 genomes from five genetically divergent human populations using long-read sequencing technology, resulting in the identification of 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these NRSs, 38.7% were common across the five populations, and 35.6% were population specific. The use of a graph-based pangenome approach allowed for the detection of 565 transcript expression quantitative trait loci on NRSs, with 426 of these being novel findings. Moreover, 26 NRS candidates displayed evidence of adaptive selection within human populations. Genes situated in close proximity to or intersecting with these candidates may be associated with metabolism and type 2 diabetes. Genome-wide association studies revealed 14 NRSs to be significantly associated with eight phenotypes. Additionally, 154 NRSs were found to be in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the understanding of human NRSs and provides novel insights into their functions, facilitating evolutionary and biomedical researches.
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Details
- Title: Subtitle
- Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles
- Creators
- Zhikun Wu - Sun Yat-sen UniversityTong Li - Sun Yat-sen UniversityZehang Jiang - Sun Yat-sen UniversityJingjing Zheng - Sun Yat-sen UniversityYizhou Gu - University of Wisconsin–MadisonYizhi Liu - Sun Yat-sen UniversityYun Liu - Sun Yat-sen UniversityZhi Xie - Sun Yat-sen University
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.52(5), pp.2212-2230
- DOI
- 10.1093/nar/gkae086
- PMID
- 38364871
- ISSN
- 0305-1048
- eISSN
- 1362-4962
- Publisher
- Oxford Univ Press
- Number of pages
- 19
- Grant note
- National Key Research and Development Program of China; National Key Research & Development Program of China; National Key Technology R&D Program Center for Precision Medicine at Sun Yat-sen University
- Language
- English
- Date published
- 03/21/2024
- Academic Unit
- Internal Medicine
- Record Identifier
- 9985178664702771
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