Sequencing genes in silico using single nucleotide polymorphisms

BMC Genetics

Research Article

John A Hansen¹  Xin Huang²  Lue Ping Zhao²  Bo Zhang²  Xinyi Cindy Zhang²  Shuying Sue Li² 

[1] Division of Clinical Research, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA;School of Medicine, University of Washington, 98195, Seattle, WA, USA;Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA;

关键词: In silico;    SNPs;    1000 Genomes Project;    multi-allelic gene;    imputation;   

DOI  :  10.1186/1471-2156-13-6

 received in 2011-10-31, accepted in 2012-01-30,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs) discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive.ResultsTo accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS), which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles) at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%). This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC) Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes.ConclusionsPrior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate genes for more detailed functional and mechanistic studies.

【 授权许可】

Unknown   
© Zhang et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.