Next-Generation Sequencing: Current Technologies and Applications

Description

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. 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