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The advances in next generation sequencing (NGS) technologies have tremendous impacts on the studies of structural and functional genomics. Sequencing-based approaches like ChIP-Seq and RNA-Seq have started taking the place of microarray experiments to study protein–DNA (deoxyribonucleic acid) interactions and transcriptomic profiling, respectively. The arrival of NGS technologies has also enabled several whole human genome resequencing studies to be completed efficiently at an affordable price. The major strengths of NGS technologies are their ultra high-throughput production, characterized by their ability to generate several hundred megabases to tens of gigabases of sequencing data per instrument run, and more importantly, the steep reduction in cost compared to the traditional Sanger sequencing method. Hence, NGS technologies have rapidly become the primary choice for large scale as well as genome-wide sequencing studies. The new sequencing-based approaches to explore structural and functional genomics have produced important information and significantly expanded our knowledge in these areas. Key concepts The rapid developments in sequencing technologies have transformed the approaches in the studies of structural and functional genomics. The arrival of next generation sequencing (NGS) technologies has started substituting traditional Sanger sequencing method in many large-scale or genome-wide sequencing studies. Shortly after the first next generation sequencer was introduced by Roche® 454 Life Science, the Genome Sequencer 20 (GS 20) System (it was subsequently replaced by GS FLX System), another two biotechnology companies also marketed their sequencing platforms: Illumina® Genome Analyzer (GA) and Applied Biosystems® (ABI) Supported Oligonucleotide Ligation Detection System (SOLiD). The major attractions of NGS technologies are their ultra high-throughput production, characterized by their ability to produce gigabases of sequencing data per instrument run, and more importantly, the steep reduction in cost compared to the traditional sequencing method. Previously, the molecular genomics studies mainly relied on microarray technologies such as gene expression microarrays and the ChIP-chip method (i.e. chromatin immunoprecipitation coupled with microarray) for genome-wide interrogation. The NGS technologies have been used in various research areas besides the standard sequencing applications such as whole genome sequencing; they have also been increasingly applied in detecting structural variations (paired-end mapping), studies of protein–DNA interactions and histone modifications (ChIP-Seq) and transcriptomic profiling of messenger RNAs (mRNAs) and noncoding RNAs (RNA-Seq). Sequencing-based approaches have already yielded numerous novel and important findings in research areas like genome-wide mapping of histone modifications and protein–DNA interactions, discovery of genetic variations and transcriptomics studies even though the approaches are still new and maturing. The NGS technologies have shown their potential of being dominant in future genomics studies. This is evident from several international projects using NGS technologies like the ENCODE Project, 1000 Genomes Project and cancers sequencing project by the International Cancer Genome Consortium. It is only a matter of time before achieving the goal of $1000 per whole genome sequencing. This should not be too far from now given the progresses in the development of third generation sequencing technologies. Although the $1000 genome will technically make sequencing of thousands of human genomes a reality, the substantial cost that will be incurred for data storage, powerful computational packages and analytical softwares has to be borne in mind. However, beyond affordability, what are left behind are the bioinformatics challenges in processing and analysing the huge amount of sequencing data. Keywords: next generation sequencing technologies; massively parallel sequencing; structural and functional genomics; ChIP-Seq; RNA-Seq |
