The expanding scope of DNA sequencing

Shendure, Jay; Aiden, E

doi:10.1038/nbt.2421

Cited by 282 publications

(193 citation statements)

References 138 publications

(145 reference statements)

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“…These techniques 'parallelise' sequencing reactions on an enormous scale, such that several sequences from smaller fragments of the DNA of interest are sequenced simultaneously and then computationally aligned in order to arrive at the final sequence result. 5,6 These techniques have now made it possible to sequence an entire human genome in a matter of weeks at a cost that is several orders of magnitude less than that of the Human Genome Project. Details of the methodology of nextgeneration sequencing are not discussed here, but for the purposes of this review it is important to emphasise that it has become affordable and efficient to produce large amounts of genomic sequencing data in a short time.…”

Section: Bioinformatics In Dna Sequencingmentioning

confidence: 99%

Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis

Upadhyay

Belbin

et al. 2014

J. Laryngol. Otol.

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Background: Advances in high-throughput molecular biology, genomics and epigenetics, coupled with exponential increases in computing power and data storage, have led to a new era in biological research and information. Bioinformatics, the discipline devoted to storing, analysing and interpreting large volumes of biological data, has become a crucial component of modern biomedical research. Research in otolaryngology has evolved along with these advances.Objectives: This review highlights several modern high-throughput research methods, and focuses on the bioinformatics principles necessary to carry out such studies. Several examples from recent literature pertinent to otolaryngology are provided. The review is divided into two parts; this first part discusses the bioinformatics approaches applied in nucleotide sequencing and gene expression analysis.Conclusion: This paper demonstrates how high-throughput nucleotide sequencing and transcriptomics are changing biology and medicine, and describes how these changes are affecting otorhinolaryngology. Sound bioinformatics approaches are required to obtain useful information from the vast new sources of data.

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Section: Bioinformatics In Dna Sequencingmentioning

confidence: 99%

Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis

Upadhyay

Belbin

et al. 2014

J. Laryngol. Otol.

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“…The maturation of NGS has driven an information boom in biology, concomitant with the development of new bioinformatics tools. As NGS and bioinformatics become increasingly widespread, these technologies are playing a growing role in fields such as human health and microbiology (Shendure and Aiden 2012). Thus, there is a need for students to gain familiarity with NGS and bioinformatics as part of modern biological science education.…”

Section: Introductionmentioning

confidence: 99%

Personal microbiomes and next-generation sequencing for laboratory-based education

Hartman

Harrington

Etson

et al. 2016

FEMS Microbiology Letters

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One sentence summary: This commentary discusses approaches and challenges for bringing personal microbiome and next-generation sequencing experiments into the classroom laboratory. Editor: Beatrix Fahnert † Mark R. Hartman, http://orcid.org/0000-0003-1564-5285 ABSTRACTSequencing and bioinformatics technologies have advanced rapidly in recent years, driven largely by developments in next-generation sequencing (NGS) technology. Given the increasing importance of these advances, there is a growing need to incorporate concepts and practices relating to NGS into undergraduate and high school science curricula. We believe that direct access to sequencing and bioinformatics will improve the ability of students to understand the information obtained through these increasingly ubiquitous research tools. In this commentary, we discuss approaches and challenges for bringing NGS into the classroom based on our experiences in developing and running a microbiome project in high school and undergraduate courses. We describe strategies for maximizing student engagement through establishing personal relevance and utilizing an inquiry-based structure. Additionally, we address the practical issues of incorporating cutting edge technologies into an established curriculum. Looking forward, we anticipate that NGS educational experiments will become more commonplace as sequencing costs continue to decrease and the workflow becomes more user friendly.

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“…In fact, if just a few years ago the complexity of generating sequencing data was more challenging and time-consuming than analyzing them, the sequencing revolution originated by the development of high-throughput sequencing instruments completely changed this scenario [2]. Actually, with single sequencing instruments capable of a throughput of 500 Gigabases of raw sequences per week, the bottleneck between sequencing and data analysis is clearly identifiable in the latter.…”

Section: Introductionmentioning

confidence: 99%

SAM-Profiler: A Graphical Tool for Qualitative Profiling of Next Generation Sequencing Alignment Data

Francesco¹,

Aless²,

'³

et al. 2013

J Comput Sci Syst Biol

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SAM/BAM alignment file formats are extensively used in virtually all the laboratories devoted to high-throughput sequencing. However, limited effort has been yet dedicated to the development of SAM/BAM quality reporting tools. To overcome this problem, we developed SAM-Profiler, a multiplatform tool dedicated to the advanced quality reporting of SAM/BAM files. SAM-Profiler performs qualitative analysis of SAM/BAM alignment data in the context of next-generation sequencing. It is implemented in C# and can be run under Windows, Linux and MacOS operative systems. Two versions are available: fully graphical, event-driven software and a command-line tool.SAM-Profiler is able to generate an extensive set of qualitative reports on SAM/BAM alignment data, among them: overall, per-base and per-chromosome read quality, mapping quality, duplicate and coverage analyses, bases distribution, perfect, proper and improper mapping, exonic, intronic, intergenic, 5` and 3` UTR coverage, mismatch distribution profile and CG distribution. In presence of paired-end sequencing experiments our tool is able to automatically report the insert size distribution and to analyze the relative pair mapping, reporting absolute and relative distribution of properly, improperly mapped, mapped/unmapped and unmapped pairs. Its modular architecture allows embedding additional analytical monitoring/reporting tools to the already developed list, allowing SAM-Profiler to grow according to the specific requests of the end-users.

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The expanding scope of DNA sequencing

Cited by 282 publications

References 138 publications

Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis

Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis

Personal microbiomes and next-generation sequencing for laboratory-based education

SAM-Profiler: A Graphical Tool for Qualitative Profiling of Next Generation Sequencing Alignment Data

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