Next-Generation Sequencing: Current Technologies and Applications

✍ Scribed by Jianping Xu (editor)

• Publisher: Caister Academic Press Limited
• Year: 2014
• Tongue: English
• Leaves: 173
• Edition: Illustrated
• Category: Library

✦ Synopsis

High-throughput, next generation sequencing (NGS) technologies are capable of producing a huge amount of sequence data in a relatively short time and have revolutionized genome research in recent years. The powerful and flexible nature of NGS has made it an indispensable tool for a broad spectrum of biological sciences, and NGS technologies have transformed scientific research in many fields. Written by experts from around the world, this book explores the most recent advances in NGS instrumentation and data analysis. The book begins with a comprehensive description of current NGS platforms, their sequencing chemistries, instrument specifications, and general workflows and procedures. A separate chapter is dedicated to low-quantity, single molecule sequencing technology. Further chapters explore the application of NGS technologies in various fields, including polymorphism detection, sRNA research, rare variant detection, large variant detection, exome sequencing, plant development studies, microbial metagenomics, and studies on the human microbiome. Practical and cutting-edge, this volume will assist all scientists who wish to apply these innovative research tools.

✦ Table of Contents

Contents
Current books of interest
Contributors
Preface
1; An Overview of Next-generation Genome Sequencing Platforms
Introduction
Second generation sequencing platforms
Third-generation sequencing platforms
Concluding remarks
2: Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies
Introduction
Materials
Methods
3: SNP Assessment on Draft Genomes from Next-generation Sequencing Data
Background
Single nucleotide polymorphisms (SNPs)
SNP calling with one sample on draft genomes with ACCUSA
Head-to-head comparisons of sequenced samples with ACCUSA 2
Conclusions
4: Processing Large-scale Small RNA Datasets in Silico
Introduction
Library preparation and sequencing
Helper tools
Analysis tools
Visualization tools
Discussion
5: Utility of High-throughput Sequence Data in Rare Variant Detection
What is a rare variant?
Why is variant detection needed?
Utility of non-HTS methods for minority and rare variant detection
Status of rare variant detection by analysis of HTS data
How much HTS data is needed to accurately detect rare variants?
Testing the feasibility of analysing HTS for rare SNP detection
Sources of errors
Experimental validation of correction approaches
Conclusions
6: Detecting Breakpoints of Insertions and Deletions from Paired-end Short Reads
Introduction
Pindel: a pattern growth method to identify precise breakpoints of indels and SVs
Performance on real data (NA18507)
Recent developments
Further advances of split-read approaches
Conclusion and future perspectives
7: Novel Insights from Re-sequencing of Human Exomes Through NGS
Introduction
The protocol
Exome capture platforms and kits
Quality control and performance evaluation
Bioinformatics analysis
Applications in human disease research
Perspective
8: Insights on Plant Development Using NGS Technologies
Introduction
Use RNA-seq to dissect transcription at the cellular resolution
Use ChIP-seq to dissect transcriptional networks
Use ChIP-seq to analyse the epigenome
Conclusions and perspectives
9: Next-generation Sequencing and the Future of Microbial Metagenomics
Introduction
Tracking microbial diversity
Applying omics technologies
Designing experiments
Modelling microbial diversity
Concluding remarks
10: Next-generation Sequencing, Metagenomes and the Human Microbiome
Introduction
Marker-specific microbial community surveys
Metagenomics – high-throughput shotgun (HTS sequencing) of microbial communities
Applications of metagenomics to the study of human health and disease
Beyond the omes – systems biology views onto the host–microbiome interactions
The new generation of cloud-based informatics solutions for next-generation sequencing
Conclusion
Index