Uncovering the Complexity of Transcriptomes with RNA-Seq

[摘要] In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousandDNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction,CNV-Seq for large genome nucleotide variations are only some of the intriguing newapplications supported by these innovative platforms. Among them RNA-Seqis perhaps the most complex NGS application. Expression levels of specific genes,differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespreadhybridization-based or tag sequence-based approaches. However, the unprecedented levelof sensitivity and the large amount of available data produced by NGS platforms provideclear advantages as well as new challenges and issues. This technology brings thegreat power to make several new biological observations and discoveries, it also requiresa considerable effort in the development of new bioinformatics tools to deal with thesemassive data files. The paper aims to give a survey of the RNA-Seqmethodology, particularly focusing on the challenges that this application presents bothfrom a biological and a bioinformatics point of view.

[学科分类] 基础医学