The impact of next-generation sequencing on genomics

Abstract

This article reviews basic concepts, general applications, and the potential impact of nextgeneration sequencing (NGS) technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demonstrated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.

Advances in genomics for flatfish aquaculture

“…An additional emerging technology is the ion torrent, considered as an intermediate approach between the SGS and TGS because it does not require any laser, fluorescent dyes or cameras, reducing drastically the costs and generating an important volume of genomic information, although it is still dependent on a PCR amplification step (Schadt et al 2010). For more technical and methodological aspects about SGS and TGS platforms, extensive reviews describing and comparing chemical costs, read performance and some other characteristics are available (Metzker 2010;Schadt et al 2010;Glenn 2011;Pareek et al 2011;Zhang et al 2011a). …”

Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing

“…Sequencing began in the 60s, although it was not until the 80s and the Sanger method [4] that gene and genome sequencing emerged. The sequencing process was a laborious manual process; following the development of automated sequencing in the late 80s the volume of information increased dramatically.…”

“…There are currently various types of NGS with different capabilities in base pairs. Zhang et al [4] describe the different manufacturers. The length of the fragments of the base pairs can vary according to the sequencing used, from 25 bp to the 500 bp used with sequencing by the Roche company, which can perform denovo sequencing [4].…”

“…Within the context of this study, the proposed system focuses on detecting relevant patterns and mutations, insertions, deletions or polymorphisms, within the sequence data taken from patient samples provided by the Cancer Institute of the University of Salamanca. The analysis of sequencing data requires various types of processes: i) assembly [4] ii) alignment [4] and iii) knowledge extraction [5] in order to analyze sequence data. The Cancer Institute of the University of Salamanca is striving to develop tools to automate the evaluation of data and to facilitate the analysis of information.…”

Subtracted Transcriptome Profile of Tiger Shrimp (Penaeus monodon) That Survived WSSV Challenge

“…Indeed, its usefulness has been proven in many aspects of shrimp health. Recent transcriptome approaches such as microarrays and next-generation sequencing (NGS) have also provided efficient applications for rapid determination of quantitative trait loci and genetic markers from immune-related genes [1,[14][15][16] because these approaches provide longer average sequence reads of 600 base pairs (bp) than traditional ones. The markers generated from these platforms may be used for a lot of genetic studies integral to taxonomy or aquaculture.…”