Genome maps across 26 human populations reveal population-specific patterns of structural variation
| Autor: | Claire Yik Lok Chung, Ahmed Naguib, Alex Hastie, Walfred Ma, Michal Levy-Sakin, Ramakrishnan Rajagopalan, Alden King-Yung Leung, Justin Sibert, Steven Pastor, Eugene Y. C. Chow, Jennifer McCaffrey, Karen H. Y. Wong, Ming Xiao, Annie Poon, Chin Lin, Han Cao, Pui-Yan Kwok, Kevin Y. Yip, Catherine J. Chu, Eleanor Young, Wei-Ping Wang, Yulia Mostovoy, Nana Jin, Ting-Fung Chan, Ernest T. Lam, Le Li |
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| Rok vydání: | 2019 |
| Předmět: |
Male
0301 basic medicine Genetic Linkage Gene Dosage General Physics and Astronomy 02 engineering and technology Genome Segmental Duplications Genomic lcsh:Science Phylogeny Segmental duplication education.field_of_study Multidisciplinary Chromosome Mapping Genomics 021001 nanoscience & nanotechnology Segmental Duplications Female 0210 nano-technology Sequence Analysis Algorithms Human Science Genomic Structural Variation Population Biology Article Chromosomes General Biochemistry Genetics and Molecular Biology Structural variation 03 medical and health sciences Genetics Humans 1000 Genomes Project education Chromosomes Human Y Base Sequence Genome Human Human Genome Computational Biology Sequence Analysis DNA DNA General Chemistry 030104 developmental biology Evolutionary biology Mutation Genomic lcsh:Q Human genome |
| Zdroj: | Nature communications, vol 10, iss 1 Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019) Nature Communications |
| ISSN: | 2041-1723 |
| Popis: | Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome. Large structural variants (SV) are understudied in human genetics research because of the difficulty to detect them in the routinely generated short-read sequencing data. Here, the authors generate optical genome maps of 154 individuals from 26 populations that allow comprehensive examination of large SVs. |
| Databáze: | OpenAIRE |
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