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Báo cáo y học: "eening the human exome: a comparison of whole genome and whole transcriptome sequencing"

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: Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. | Cirulli et al. Genome Biology 2010 11 R57 http genomebiology.eom 2010 11 5 R57 w Genome Biology RESEARCH _ Open Access Screening the human exome a comparison of whole genome and whole transeriptome sequencing Elizabeth TCirulli21 Abanish Singh 1 Kevin VShianna 1 Dongliang Ge1 Jason P Smith1 Jessica M Maia1 Erin L Heinzen1 James J Goedert2 David B Goldstein 1 for the Center for HIV AIDS Vaccine Immunology CHAVI Abstract Background There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible whole-genome sequencing whole-exome sequencing using exon capture methods and RNA-Seq. While whole-genome sequencing is the most complete it remains sufficiently expensive that cost effective alternatives are important. Results Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40 of exonic variants identified by whole genome sequencing were captured using RNA-Seq this number rose to 81 when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data especially at higher levels of coverage. Conclusions We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels. Background The study