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Báo cáo y học: "Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. | Bainbridge et al. Genome Biology 2011 12 R68 http genomebiology.eom 2011 12 7 R68 Genome Biology RESEARCH Open Access Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities 1.2 1 1 1 1 3 Matthew N Bainbridge Min Wang Yuanqing Wu Irene Newsham Donna M Muzny John L Jefferies Thomas J Albert4 Daniel L Burgess4 and Richard A Gibbs 1 Abstract Background Enrichment of loci by DNA hybridization-capture followed by high-throughput sequencing is an important tool in modern genetics. Currently the most common targets for enrichment are the protein coding exons represented by the consensus coding DNA sequence CCDS . The CCDS however excludes many actual or computationally predicted coding exons present in other databases such as RefSeq and Vega and non-coding functional elements such as untranslated and regulatory regions. The number of variants per base pair variant density and our ability to interrogate regions outside of the CCDS regions is consequently less well understood. Results We examine capture sequence data from outside of the CCDS regions and find that extremes of GC content that are present in different subregions of the genome can reduce the local capture sequence coverage to less than 50 relative to the CCDS. This effect is due to biases inherent in both the Illumina and SOLiD sequencing platforms that are exacerbated by the capture process. Interestingly for two subregion types microRNA and predicted exons the capture process yields higher than expected coverage when compared to whole genome sequencing. Lastly we examine the variation present in non-CCDS regions and find that predicted exons as well as exonic regions specific to RefSeq and Vega show much higher variant densities than the CCDS. Conclusions We show that regions outside of the CCDS perform less efficiently in capture sequence experiments. Further we show that the variant density in computationally predicted exons is more than 2.5-times .