Special Issue "Next Generation DNA Sequencing"

Guest Editor
Dr. Paul Richardson
Progentech Limited, 5885 Hollis St., Suite 155, Emeryville, CA 94608, USA
Website: http://www.progentech.com/about-us/management
E-Mail:
Interests: microbial genomics; technology development; infectious diseases; gene expression

Dear Colleagues,

We are currently in the midst of a revolution in DNA sequencing that promises unprecedented access to genetic data. Next Generation Sequencing (NGS) and follow-on technologies such as single molecule sequencing (next-next gen or 3rd generation) instruments and methods are advancing rapidly. These advances open the door to new applications for sequencing such as large-scale association studies, comparative genomics, metagenomics and the study of ancient DNA. These technologies have also been used in chromatin immunoprecipitation studies to determine DNA binding sites and quantitative RNA expression analysis by sequencing. These instrument platforms create unique challenges both upstream and downstream of the data generation. Improved methods for library construction and amplification strategies to produce more uniform and complete coverage are required. Methods are also evolving for the processing and analysis of extremely large numbers (often short) reads to better understand quality, improve alignments and generate whole-genome assemblies. Given the huge impact of these developments, a special issue of the journal Genes is being issued to explore the methods and applications of these new sequencing technologies. Authors are encouraged to submit original manuscripts describing utilization of Next Generation Sequencing to answer scientific questions. Also encouraged are papers describing new methods or instruments, and reviews or comparisons of Next Generation Sequencing technologies as well as manuscripts dealing with bioinformatic methods of analysis.

Dr. Paul Richardson
Guest Editor

Submission Information

All manuscripts should be submitted to genes@mdpi.org with a copy to the Guest Editor. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues, to be published in 2010, the Article Processing Charges (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

• DNA Sequencing
• next generation sequencing
• single molecule sequencing
• massively parallel sequencing
• metagenomics
• ChiP-Seq
• ancient DNA
• digital gene expression

Type of Paper: Review
Title: The Application of Next Generation Sequencing in DNA Methylation Analysis
Authors: Yingying Zhang and Albert Jeltsch; E-Mail: a.jeltsch@jacobs-university.de
Affiliation: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
Abstract: DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. Its pattern is highly variable among cell types, developmental stages, disease processes and genetic factors, which brings considerable theoretical and technological challenges for the comprehensive understanding of this essential modification underlying epigenetic regulation mechanisms. Recently various high-throughput approaches based on next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation in mammals and plants, which will be reviewed here. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. They will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states.

Type of Paper: Review
Title: Next Generation DNA Sequencing and the Promise of Genomic Medicine
Authors: Matthew W. Anderson and Iris Schrijver
Affiliation: Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5627, USA; E-Mails: mwanders@stanford.edu (M. A.); schrijver@stanfordmed.org (I. S.)
Abstract: In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpretation, laboratory workflow, data storage, and ethical considerations. This review describes the current high-throughput sequencing platforms commercially available, and compares the inherent advantages and disadvantages of each. The potential applications for clinical diagnostics are considered, as well as the need for software and analysis tools to interpret the overwhelming amount of data generated. Finally, we discuss the clinical and ethical implications of the wealth of genetic information generated by these methods. Despite these concerns, we anticipate that the evolution and refinement of high-throughput DNA sequencing technologies will catalyze a new era of personalized medicine based on individualized genomic analysis.

Type of Paper: Review
Title: Statistical Issues in the Analysis of Next-Generation Sequencing Data
Authors: Debashis Ghosh ¹ and Zhaohui Qin ²
Affiliations: ¹ Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802, USA; E-Mail: ghoshd@psu.edu
² Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Abstract: The recent arrival of ultra-high throughput, next-generation sequencing (NGS) technologies has revolutionized the field of genomics by allowing for rapid and relatively inexpensive sequencing of billions of bases. The rapid deployment of NGS to a variety of sequencing-based experiments has resulted in the generation of massive amounts of sequencing data. To better understand and more effectively process this new type of data, a variety of increasingly sophisticated algorithms and software tools are emerging to help with the analysis stages of the NGS applications. In this article, we aim to identify the critical challenges that arise from the different stages of NGS data analysis and provide an objective overview of what have been achieved in existing research. At the same time, we highlight selected areas that need much further research to improve our capabilities to delineate the most information from NGS data.

Type of Paper: Article
Title: De Novo Sequence Assembly Challenges Using Next Generation Sequencing Data: A Computer Simulation Study
Authors: Bjarne Knudsen ¹, Roald Forsberg ¹ and Michael M. Miyamoto ²
Affiliations: ¹ CLC bio, Finlandsgade 10-12, Katrinebjerg, 8200 Aarhus N, Denmark
² University of Florida, Department of Biology, Gainesville FL 32611, USA; E-Mail: miyamoto@ufl.edu
Abstract: to be added soon

Type of Paper: Review
Title: Next Generation Sequencing of miRNAs – Strategies, Resources, and Methods
Authors: Susanne Motameny ¹, Steffi Wolters ², Peter Nürnberg ¹ and Björn Schumacher ²
Affiliations: ¹Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
² Cologne Excellence Cluster for Cellular Stress Responses in Aging Associated Diseases (CECAD), 50674 Cologne, Germany; E-Mail: bjoern.schumacher@uni-koeln.de
Abstract: miRNAs have recently been demonstrated to play a central role in regulating gene expression in many organisms. With the advent of next generation sequencing, new opportunities have opened up to identify and quantify miRNAs and elucidate their function. The unprecedented sequencing depth reached by next generation sequencing technologies makes it possible to get a comprehensive overview of the miRNA landscape of a sample with just a single experiment but also poses new challenges for data analysis. We provide an overview of the strategies used for miRNA sequencing, public miRNA resources, and useful methods and tools that are available for data analysis.