De novo assembly of a haplotype-resolved human genome
| Autor: | Yu Wang, Haodong Huang, Honglong Wu, Lars Bolund, Laurent C. A. M. Tellier, Xiuqing Zhang, Zheng Huang, Hongzhi Cao, Rasmus Nielsen, Xin Tong, Li Yue, Bo Li, Xiao Liu, Siyang Liu, Ruibang Luo, Yuhui Sun, Guangzhu He, Sun Jing, Shujia Huang, Dan Chen, Yingrui Li, Xun Xu, Jian Li, Songgang Li, Weihua Huang, Jun Wang, Qiang Feng, Anders Krogh, Peng Sun, Karsten Kristiansen, Snezana Drmanac, Gane Ka-Shu Wong, Binghang Liu, Radoje Drmanac, Yinlong Xie, Jian Wang, Hailong Yang, Peng Gao, Huanming Yang, Fang Yang, Hancheng Zheng |
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| Rok vydání: | 2015 |
| Předmět: |
Cancer genome sequencing
Genome evolution Genotype Biomedical Engineering Bioengineering Biology ENCODE Polymorphism Single Nucleotide Applied Microbiology and Biotechnology Genome Asian People Gene density Humans Precision Medicine Genetics Base Sequence Genome Human Chromosome Mapping High-Throughput Nucleotide Sequencing Sequence Analysis DNA Genome project Diploidy Phenotype Haplotypes Molecular Medicine Human genome Biotechnology Reference genome |
| Zdroj: | Cao, H, Wu, H, Luo, R, Huang, S, Sun, Y, Tong, X, Xie, Y, Liu, B, Yang, H, Zheng, H, Li, J, Li, B, Wang, Y, Yang, F, Sun, P, Liu, S, Gao, P, Huang, H, Sun, J, Chen, D, He, G, Huang, W, Huang, Z, Li, Y, Tellier, L C A M, Liu, X, Feng, Q, Xu, X, Zhang, X, Bolund, L, Krogh, A, Kristiansen, K, Drmanac, R, Drmanac, S, Nielsen, R, Li, S, Wang, J, Yang, H, Li, Y, Wong, G K-S & Wang, J 2015, ' De novo assembly of a haplotype-resolved human genome ', Nature Biotechnology, vol. 33, no. 6, pp. 617-22 . https://doi.org/10.1038/nbt.3200 |
| ISSN: | 1546-1696 1087-0156 |
| DOI: | 10.1038/nbt.3200 |
| Popis: | The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine. |
| Databáze: | OpenAIRE |
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