A novel method for nucleic acid sequence determination

Bains, William; Smith, Geoff

doi:10.1016/s0022-5193(88)80246-7

Cited by 277 publications

(109 citation statements)

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“…Then, researchers began to work on a reciprocal technique, in which the known genes or fragments were immobilized on a substrate, and the solution to be queried was labeled and hybridized to the surface (Bains and Smith 1988;Drmanac et al 1989). …”

Section: Hybridization-based Transcriptome Platformmentioning

confidence: 99%

Advancing transcriptome platforms

Shi

2011

Nat Prec

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During the last decade of years, remarkable technological innovations have emerged that allow the direct or indirect determination of transcriptome at unprecedented scale and speed. Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome. Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently developed RNA-Seq (RNA sequencing) based platform. Especially, the nextgeneration technologies make a revolution in assessing the entire transcriptome via 1

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Section: Hybridization-based Transcriptome Platformmentioning

confidence: 99%

Advancing transcriptome platforms

Shi

2011

Nat Prec

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“…Three DNA sequencing platforms are now being used to scan for mutations and polymorphisms. These include Sanger DNA sequencing [22] hybridizationbased sequencing [4,6,10,23,24] and Pyrosequencing [17,20]. Pyrosequencing is based on the detection of released pyrophosphate (PPi) during DNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing

Ronaghi

Elahi

2002

Comp Funct Genom

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Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how to reduce the cost for large-scale analysis. Copyright # 2002 John Wiley & Sons, Ltd.Keywords: SNP; Pyrosequencing; re-sequencing; bioluminescence; haplotyping; mutation detection; luciferase Determination of mutations and polymorphisms in a genome is one of the most important tasks in the studies of biological systems today. Three DNA sequencing platforms are now being used to scan for mutations and polymorphisms. These include Sanger DNA sequencing [22] hybridizationbased sequencing [4,6,10,23,24] and Pyrosequencing [17,20]. Pyrosequencing is based on the detection of released pyrophosphate (PPi) during DNA synthesis. In a cascade of enzymatic reactions, visible light proportional to the number of incorporated nucleotides is generated (Figure 1). The cascade starts with a nucleic acid polymerization reaction in which inorganic pyrophosphate (PPi) is released as a result of nucleotide incorporation by polymerase. The released PPi is subsequently converted to ATP by ATP sulfurylase which provides the energy to luciferase to oxidize luciferin and generate light. Since the added nucleotide is known, the sequence of the template can be determined (Figure 1). Pyrosequencing has the potential advantages of accuracy, flexibility, parallel processing and can be easily automated. Furthermore it dispenses with the need for labelled primers, labelled nucleotides and gel-electrophoresis [21]. The methodological performance of Pyrosequencng in determination of difficult secondary DNA Current Pyrosequencing strategy using a commercial machine allows more than 50 nucleotides to be de novo sequenced routinely. Pyrosequencing may be the method of choice for sequencing of difficult secondary DNA structures which cannot be sequenced by conventional sequencing. In this review we discuss the use of Pyrosequencing for mutation scanning, SNP scanning and haplotyping, and describe the cost reduction efforts for largescale studies. Re-sequencing for mutation discoveryThe ability to sequence a large number of DNA samples rapidly and accurately for detection of all possible mutations is a critical goal in biomedicine. DNA mutations can be classified as known or unknown mutations. If the mutation is known, the region containing the mutation can be analyzed at or nearby the mutation site. If the mutation is unknown, re-sequencing of the region for determination of the nature of the mutation is required. When DNA from biopsy material is being resequenced, a quantitative method for determining the ratio between wild and mutated template is desired. When analyzin...

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“…Sequencing by hybridization (SBH) [3,5,7,8,11,13] is a proposed approach to DNA sequencing where a set of single-stranded fragments (typically all possible 4 k oligonucleotides of length k) are attached to a substrate, forming a sequencing chip. A solution of single-stranded target DNA fragments are exposed to the chip.…”

Section: Introductionmentioning

confidence: 99%

Restricting SBH Ambiguity via Restriction Enzymes

Skiena

Snir

2002

Lecture Notes in Computer Science

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Abstract. The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string's RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.

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A novel method for nucleic acid sequence determination

Cited by 277 publications

References 9 publications

Advancing transcriptome platforms

Advancing transcriptome platforms

Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing

Restricting SBH Ambiguity via Restriction Enzymes

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