Journal article
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
Y Li, H Zheng, R Luo, H Wu, H Zhu, R Li, H Cao, B Wu, S Huang, H Shao, H Ma, F Zhang, S Feng, W Zhang, H Du, G Tian, J Li, X Zhang, S Li, L Bolund Show all
Nature Biotechnology | NATURE PUBLISHING GROUP | Published : 2011
DOI: 10.1038/nbt.1904
Abstract
Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small-and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1-23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genome..
View full abstractGrants
Awarded by Natur og Univers, Det Frie Forskningsråd
Funding Acknowledgements
This work was supported by a National Basic Research Program of China (973 program no. 2011CB809200), the National Natural Science Foundation of China (30725008; 30890032; 30811130531; 30221004), the Chinese 863 program (2006AA02Z177; 2006AA02Z334; 2006AA02A302; 2009AA022707), the Shenzhen Municipal Government of China (grants JC200903190767A; JC200903190772A; ZYC200903240076A; CXB200903110066A; ZYC200903240077A; ZYC200903240 076A and ZYC200903240080A) and the Ole Romer grant from the Danish Natural Science Research Council. This project is also funded by the Shenzhen Municipal Government and the Local Government of Yantian District of Shenzhen. The 1000 Genomes Project Consortium provided the data for population analysis. AIFB is supported by Diabetes UK, the Wellcome Trust, the Medical Research Council and the Comprehensive Biomedical Research Centre, Imperial College Healthcare NHS Trust. Thanks to X. Wang from School of Biosciences & Bioengineering, SCUT, for his excellent coordination. Thanks to J. El-Sayed Moustafa for her help analyzing the experimental validation data. L. Goodman, S. Edmunds and A. Basford edited the manuscript.