Abstract
We have used targeted genomic sequencing of high-complexity DNA pools based on long-range PCR and deep DNA sequencing by the SOLiD technology. The method was used for sequencing of 286 kb from four chromosomal regions with quantitative trait loci (QTL) influencing blood plasma lipid and uric acid levels in DNA pools of 500 individuals from each of five European populations. The method shows very good precision in estimating allele frequencies as compared with individual genotyping of SNPs (r2=0.95, P<10−16). Validation shows that the method is able to identify novel SNPs and estimate their frequency in high-complexity DNA pools. In our five populations, 17% of all SNPs and 61% of structural variants are not available in the public databases. A large fraction of the novel variants show a limited geographic distribution, with 62% of the novel SNPs and 59% of novel structural variants being detected in only one of the populations. The large number of population-specific novel SNPs underscores the need for comprehensive sequencing of local populations in order to identify the causal variants of human traits.
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Acknowledgements
The SOLiD DNA sequencing and Taqman genotyping was performed by the Uppsala Genome Center, funded by the Knut and Alice Wallenberg Foundation (CMS), The Swedish Natural Sciences Research Council (SNISS) and Science for Life Laboratory, Uppsala. This work was supported by the following grants and agencies: Swedish Medical Sciences Research Council, the Foundation for Strategic Research (SSF), the Linneaus Centre for Bioinformatics (LCB), European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947), The Netherlands Organisation for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043), European Commission FP7 grant LipidomicNet (2007-202272), NWO, ErasmusMC and the Centre for Medical Systems Biology (CMSB), the Ministry of Health and Department of Educational Assistance, University and Research of the Autonomous Province of Bolzano, and the South Tyrolean Sparkasse Foundation, the Scottish Executive Health Department and the Royal Society, the Medical Research Council UK, Ministry of Science, Education, and Sport of the Republic of Croatia (number 108-1080315-0302), Deutsche Forschungsgemeinschaft, the German Federal Ministry of Education and Research in the context of the German National Genome Research Network and Cardiogenics (EU-funded integrated project LSHM-CT- 2006-037593), the GSF-National Research Centre for Environment and Health funded by the German Federal Ministry of Education and Research and of the State of Bavaria.
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Zaboli, G., Ameur, A., Igl, W. et al. Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits. Eur J Hum Genet 20, 77–83 (2012). https://doi.org/10.1038/ejhg.2011.138
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DOI: https://doi.org/10.1038/ejhg.2011.138
