1. Introduction In the early 1990s, a plethora of strategies for genome sequencing were proposed as part of the initial phases of the Human Genome Project (HGP). Each strategy relied to varying extents on three types of maps: (1) genetic and radiation hybrid maps consist of sequence tagged site (STS) markers of known order throughout […]

Hierarchical, ordered mapped large insert clone shotgun sequencing (Genomics)

The underlying concept of employing dideoxynucleotides as chain terminators in the DNA sequencing reaction, to create a replicated nested fragment set that is size fractionated and detected, has changed little since it was first reported by Sanger et al. in 1970 (Sanger et al., 1977). In contrast, the detailed methods implemented in the laboratory to […]

Genome sequencing of microbial species (Genomics)

1. Whole-genome shotgun cloning: a revolution in the microbial field Microbes account for most of life on earth and are critical to its ecological balance. However, researchers have only scratched the surface of the tremendous biodiversity that these organisms display. Less than 1% has been cultured – only a minute proportion of the microbial diversity […]

Sequencing templates – shotgun clone isolation versus amplification approaches (Genomics)

1. Introduction High-quality DNA is essential to obtaining the greatest success in DNA sequencing. Sequencing quality DNA should contain the lowest possible level of contaminating host DNA, have consistent yields from sample to sample, and be in sufficient quantities to perform multiple sequence reactions. Many thousands of clones are required whether a whole-genome shotgun or […]

Robotics and automation (Genomics)

1. Introductory remarks Reflecting on the past 15 years of the history of large-scale DNA sequencing, it is incredible to realize just how far this discipline has progressed in a relatively short period of time. The efforts, hopes, fears, and failures of many molecular biologists, engineers, and others have been played out in the arena […]

Microelectrophoresis devices for DNA sequencing (Genomics)

1. Introduction Extensive applications in genomics and biomedicine remain inaccessible because of the current cost of DNA sequencing technology. Commercial capillary arrays enabled the Human Genome Project but currently define the, often, prohibitive cost structure of sequencing. Microelectromechanical systems (MEMS) have been proposed as one technical approach to a significant near-term advance. The often-cited intrinsic […]

Real-time DNA sequencing (Genomics)

1. Introduction DNA sequence information provides insights into a wide range of biological processes. The order of bases in DNA implies the order of bases in RNA and, consequently, the amino acid sequence of protein. DNA sequence specifies a molecular program that can lead to normal development or the manifestation of a genetic disease such […]

Single molecule array-based sequencing (Genomics)

1. Introduction Hidden within an individual’s genomic sequence are the genetic instructions for the entire repertoire of cellular components that determine the complexities of biological systems. Unraveling genomic structure and characterizing the functional elements from within the code will allow connections to be made between the genetic blueprint, transcribed information, and the resulting systems biology, […]

Genome mapping overview (Genomics)

1. Introduction True physical maps, for example, fingerprint maps in which each clone is “fingerprinted” on the basis of the pattern of fragments generated by a restriction enzyme digest, of large-insert molecular clones have had a tremendous impact upon large-scale genomic DNA sequencing. The physical map of the human genome (McPherson et al., 2001) provided […]

Linking DNA to production: the mapping of quantitative trait loci in livestock (Genomics)

1. Introduction The world’s livestock populations provide a considerable resource with which functions can be assigned to genes. Unique populations have resulted from centuries of genetic selection focused on specific traits such as milk or meat production, fertility, and conformation, to name a few. Livestock production is of significant economic importance worldwide, and animal breeders […]