Special Issue: Next Generation DNA Sequencing

Next Generation Sequencing (NGS) refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger) sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance). The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche), Illumina (formerly Solexa) Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies) and the Heliscope (Helicos Corporation). The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. In this special issue, nine papers review and demonstrate the utility and potential of next generation sequencing. One of the biggest consequences with NGS technologies is how to deal with all of the data produced by these platforms. Magi et al. [1] review the software tools available for the multiple functions needed to process and interpret the huge amounts of data produced by these instruments. Sequence alignment to a reference, polymorphism detection, de novo assembly and visualization software are covered in this paper. Knudsen and colleagues [2] introduce a computer simulator that utilizes real and simulated reads to assess the effects of different factors and strategies for utilizing NGS to perform de novo assemblies. This is presently a particular challenge for the generally short (sometimes unpaired) reads produced by NGS Technologies. Another review article [3] on bioinformatic issues with NGS data focuses on statistical methods for analysis of Chip-Seq data as well as RNA data generated by these methods. NGS platforms are particularly suited to the use of ChIP-Seq methods as an alternative to ChIP-ChIP methods for identification of transcription factor binding sites.