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: Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. | Turro et al. Genome Biology 2011 12 R13 http 2011 12 2 R13 Genome Biology METHOD Open Access Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads 1 2 3 1 11 Ernest Turro Shu-Yi Su Ângela Gongalves Lachlan JM Coin Sylvia Richardson Alex Lewin Abstract We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the expression of haplotype-specific isoforms. If unknown the two parental isoform sequences can be individually reconstructed. A new statistical method MMSEQ deconvolves the mapping of reads to multiple transcripts isoforms or haplotype-specific isoforms . Our software can take into account non-uniform read generation and works with paired-end reads. Background High-throughput sequencing of RNA known as RNA-seq is a promising new approach to transcriptome profiling. RNA-seq has a greater dynamic range than microarrays which suffer from non-specific hybridization and saturation biases. Transcriptional subsequences spanning multiple exons can be directly observed allowing more precise estimation of the expression levels of splice variants. Moreover unlike traditional expression arrays RNA-seq produces sequence information that can be used for genotyping and phasing of haplotypes thus permitting inferences to be made about the expression of each of the two parental haplotypes of a transcript in a diploid organism. The first step in RNA-seq experiments is the preparation of cDNA libraries whereby RNA is isolated fragmented and synthesized to cDNA. Sequencing of one or both ends of the fragments then takes place to produce millions of short reads and an associated base call uncertainty measure for each position in each read. The reads are then aligned usually allowing for sequencing errors and polymorphisms to a set of reference chromosomes or transcripts. The alignments of the reads are the
