Издательство Artech House, 2008, -275 pp.
The dideoxynucleotide termination DNA sequencing technology invented by Fred Sanger and colleagues, published in 1977, formed the basis for DNA sequencing from its inception through 2004 [1]. Originally based on radioactive labeling, the method was automated by the use of fluorescent labeling coupled with excitation and detection on dedicated instruments, with fragment separation by slab gel [2] and ultimately by capillary gel electrophoresis. A variety of molecular biology, chemistry, and enzymology-based improvements have brought Sanger’s approach to its current state of the art. By virtue of economies of scale, high-throughput automation and reaction optimization, large sequencing centers have decreased the cost of a fluorescent Sanger sequencing reaction to around $
0.30. However, it is likely that only incremental cost decreases will continue to be achieved for Sanger sequencing in its current manifestation. This fact, coupled with the ever-increasing need for DNA sequencing toward a variety of biomedical (and other) studies, has resulted in a rapid phase of technology development of so-called next generation or massively parallel sequencing technologies, that will revolutionize DNA sequencing as we now know it. Along with this revolution will come a significant and potentially unanticipated impact
It is perhaps interesting to evaluate the scientific underpinnings that have led to the recent revolution in DNA sequencing technology. With the completion of the reference human genome [3, 4], human geneticists and others began to question the nature and extent of genome-wide interindividual genomic variation. This concept of strain-to-reference comparison was not a novel one—certainly microbiologists had been studying the genomic differences between reference and pathogenic (clinical) strains of viruses and bacteria for many years, largely enabled by the ever-increasing availability of genome sequences for these organisms. Transitioning this concept to larger and more complex genomes simply is a matter of increasing the scale of comparison, since the human genome is approximately 1,000-fold larger than that of the average bacterium. It is also appropriate to note that much more focused strain-to-reference comparisons of human sequences have been pursued for many years in many studies, using PCR-based resequencing approaches. Here, PCR with genome-unique primers is utilized to selectively amplify the same region from many individual genomes and each resulting product is sequenced. A comparison of all sequences to the human reference can subsequently highlight common and rare mutations that may predispose to the disease state, predict outcome, or aid in the identification of specific treatments [5–13]. on sequencing-supportive infrastructures, namely, the computational hardware and software required to process and interpret these data.
Part I The New DNA Sequencing Technology
An Overview of New DNA Sequencing Technology
Array-Based Pyrosequencing Technology
The Role of Resequencing Arrays in Revolutionizing DNA Sequencing
Polony Sequencing
Genome Sequencing: A Complex Path to Personalized Medicine
Part II Genome Sequencing and Fragment Assembly 77
Overview of Genome Assembly Techniques
Fragment Assembly Algorithms
Assembly for Double-Ended Short-Read Sequencing Technologies
Part III Beyond Conventional Genome Sequencing
Genome Characterization in the Post–Human Genome Project Era
The Haplotyping Problem: An Overview of Computational Models and Solutions
Analysis of Genomic Alterations in Cancer
High-Throughput Assessments of Epigenomics in Human Disease
Comparative Sequencing, Assembly, and Anchoring
The dideoxynucleotide termination DNA sequencing technology invented by Fred Sanger and colleagues, published in 1977, formed the basis for DNA sequencing from its inception through 2004 [1]. Originally based on radioactive labeling, the method was automated by the use of fluorescent labeling coupled with excitation and detection on dedicated instruments, with fragment separation by slab gel [2] and ultimately by capillary gel electrophoresis. A variety of molecular biology, chemistry, and enzymology-based improvements have brought Sanger’s approach to its current state of the art. By virtue of economies of scale, high-throughput automation and reaction optimization, large sequencing centers have decreased the cost of a fluorescent Sanger sequencing reaction to around $
0.30. However, it is likely that only incremental cost decreases will continue to be achieved for Sanger sequencing in its current manifestation. This fact, coupled with the ever-increasing need for DNA sequencing toward a variety of biomedical (and other) studies, has resulted in a rapid phase of technology development of so-called next generation or massively parallel sequencing technologies, that will revolutionize DNA sequencing as we now know it. Along with this revolution will come a significant and potentially unanticipated impact
It is perhaps interesting to evaluate the scientific underpinnings that have led to the recent revolution in DNA sequencing technology. With the completion of the reference human genome [3, 4], human geneticists and others began to question the nature and extent of genome-wide interindividual genomic variation. This concept of strain-to-reference comparison was not a novel one—certainly microbiologists had been studying the genomic differences between reference and pathogenic (clinical) strains of viruses and bacteria for many years, largely enabled by the ever-increasing availability of genome sequences for these organisms. Transitioning this concept to larger and more complex genomes simply is a matter of increasing the scale of comparison, since the human genome is approximately 1,000-fold larger than that of the average bacterium. It is also appropriate to note that much more focused strain-to-reference comparisons of human sequences have been pursued for many years in many studies, using PCR-based resequencing approaches. Here, PCR with genome-unique primers is utilized to selectively amplify the same region from many individual genomes and each resulting product is sequenced. A comparison of all sequences to the human reference can subsequently highlight common and rare mutations that may predispose to the disease state, predict outcome, or aid in the identification of specific treatments [5–13]. on sequencing-supportive infrastructures, namely, the computational hardware and software required to process and interpret these data.
Part I The New DNA Sequencing Technology
An Overview of New DNA Sequencing Technology
Array-Based Pyrosequencing Technology
The Role of Resequencing Arrays in Revolutionizing DNA Sequencing
Polony Sequencing
Genome Sequencing: A Complex Path to Personalized Medicine
Part II Genome Sequencing and Fragment Assembly 77
Overview of Genome Assembly Techniques
Fragment Assembly Algorithms
Assembly for Double-Ended Short-Read Sequencing Technologies
Part III Beyond Conventional Genome Sequencing
Genome Characterization in the Post–Human Genome Project Era
The Haplotyping Problem: An Overview of Computational Models and Solutions
Analysis of Genomic Alterations in Cancer
High-Throughput Assessments of Epigenomics in Human Disease
Comparative Sequencing, Assembly, and Anchoring