Open Access Medical Books

DNA SEQUENCING – METHODS AND APPLICATIONS

DNA SEQUENCING

Edited by Anjana Muns .

184 pages . 
Open Access . 

More than a quarter of a century earlier the story of DNA sequencing began when Sanger’s studies of insulin first demonstrated the importance of sequence in biological macromolecules. Although two different DNA sequencing methods have been developed during the same period, Sanger’s dideoxy chain-termination sequencing method has became the method of choice over the Maxam–Gilbert method. The complete sequence of oX-174 was published in 1977 and then revised slightly in the following year by dideoxy method. It demonstrated that the DNA sequence could tell a fascinating story based upon the interpretation of the sequence in terms of the genetic code. Recently several next generation high throughput DNA sequencing techniques have arrived on the scene and are opening fascinating opportunities in the fields of biology and medicine.
This book, “DNA Sequencing - Methods and Applications” illustrates methods of DNA sequencing and its application in plant, animal and medical sciences. This book has two distinct sections. The first one includes 2 chapters devoted to the DNA sequencing methods and the second one includes 6 chapters focusing on various applications of this technology. The content of the articles presented in the book is guided by the knowledge and experience of the contributing authors. This book is intended to serve as an important resource and review to the researchers in the field of DNA sequencing.
An overview of DNA sequencing technologies right from the Sanger’s method to the next generation high throughput DNA sequencing techniques including massively parallel signature sequencing, polony sequencing, pyrosequencing, Illumina Sequencing, SOLiD sequencing etc. has been presented in chapter 1. Chapter 2 reviews how Hot Start-7-deaza-dGTP improves Sanger’s dideoxy sequencing data of GC rich template DNA.
Chapter 3 demonstrates how the use of sequencing methods in combination with strategies in breeding and molecular genetic modifications has contributed to our knowledge of plant genetics and remarkable increase in agricultural productivity.
Chapter 4 provides information on applications of DNA sequencing in crop protection. This chapter highlights the perspectives for new sustainable and environmental friendly strategies for controlling pests and diseases of crop plants.
Chapter 5 has discussed the application of DNA sequencing in improving the breeding strategies of farm animals. The development of molecular markers using DNA sequencing serves as an underlying tool, for geneticists and breeders to create desirable farm animals.
Chapter 6 aims at showing how DNA sequencing technology has reboosted rodent systematics leading to a much better supported classification of this order. The molecular data generated by DNA sequencing has played an important role in rodent systematics over the last decades indicating the importance of this kind of information in evolutionary biology as a whole.
Chapter 7 has discussed the application of pooled DNA sequencing in disease association studies. It is a cost effective strategy for genome-wide association studies (GWAS) and successfully identifies hundreds of variants associated with complex traits. Some strategies of pooling design including PI- deconvolution shiftedtransversal design, multiplex scheme and overlapping pools to recover linkage disequilibrium information have also been introduced. Statistical methods for the detection of variants and case-control association studies accounting for high levels of sequencing errors have been discussed.
Chapter 8 focuses on the development of nucleic acid-aptamers and the outlook for related technologies. Aptamers can be readily amplified by PCR and decoded by sequencing and it is possible to apply them as molecular tags to quantitative bimolecular analysis and single cell analysis.
The scientific usefulness of DNA sequencing continues to be proven, and the number of sequenced and catalogued genomes has grown more than five times from where it was at the middle of the decade.


Anjana Munshi

Department of Molecular Biology,
Institute of Genetics and Hospital for Genetic Diseases, Hyderabad,
India 
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CONTENTS :


Section 1 : Methods of DNA Sequencing .


1 DNA Representation 3 Bharti Rajendra Kumar

2 Hot Start 7-Deaza-dGTP Improves Sanger Dideoxy Sequencing Data of GC-Rich Targets 15 Sabrina Shore, Elena Hidalgo Ashrafi and Natasha Paul


Section 2 : Applications of DNA Sequencing .


3 Sequencing Technologies and  Their Use in Plant Biotechnology and Breeding 35  Victor Llaca

4 DNA Sequencing and Crop Protection 61  Rosemarie Tedeschi

5 Improvement of Farm Animal Breeding by DNA Sequencing 85  G. Darshan Raj

6 The Input of DNA Sequences to  Animal Systematics: Rodents as Study Cases 103  Laurent Granjon and Claudine Montgelard

7 The Application of  Pooled DNA Sequencing in Disease Association Study 141  Chang-Yun Lin and Tao Wang

8 Nucleic Acid Aptamers as Molecular Tags for  Omics Analyses Involving Sequencing 157  Masayasu Kuwahara and Naoki Sugimoto .




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