Accurate sequencing by hybridization for DNA diagnostics and individual genomics

Drmanac, Snezana; Kita, David; Labat, Ivan; Hauser, Brian; Schmidt, Carl J.; Burczak, John D.; Drmanac, Radoje

doi:10.1038/nbt0198-54

Cited by 151 publications

(76 citation statements)

References 11 publications

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“…To overcome the limitations of the current sequencing technology based on electrophoresis using laser-induced fluorescence detection (3)(4)(5), a variety of new DNA-sequencing methods have been explored. Such techniques include pyrosequencing (6), MS sequencing (7-9), sequencing by hybridization (10), sequence-specific detection of singlestranded DNA using engineered nanopores (11), and sequencing of single DNA molecules (12) and polymerase colonies (13).…”

mentioning

confidence: 99%

Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry

Seo

Bai

Ruparel

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

125

105

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DNA sequencing by synthesis on a solid surface offers new paradigms to overcome limitations of electrophoresis-based sequencing methods. Here we report DNA sequencing by synthesis using photocleavable (PC) fluorescent nucleotides [dUTP-PC-4,4-difluoro-4-bora-3␣,4␣-diaza-s-indacene (Bodipy)-FL-510, dCTP-PC-Bodipy-650, and dUTP-PC-6-carboxy-X-rhodamine (ROX)] on a glass chip constructed by 1,3-dipolar azide-alkyne cycloaddition coupling chemistry. Each nucleotide analogue consists of a different fluorophore attached to the base through a PC 2-nitrobenzyl linker. We constructed a DNA microarray by using the 1,3-dipolar cycloaddition chemistry to sitespecifically attach azido-modified DNA onto an alkyne-functionalized glass chip at room temperature under aqueous conditions. After verifying that the polymerase reaction could be carried out successfully on the above-described DNA array, we then performed a sequencing reaction on the chip by using a self-primed DNA template. In the first step, we extended the primer using DNA polymerase and dUTP-PC-Bodipy-FL-510, detected the fluorescent signal from the fluorophore Bodipy-FL-510, and then cleaved the fluorophore using 340 nm UV irradiation. This process was followed by extension of the primer with dCTP-PC-Bodipy-650 and the subsequent detection of the fluorescent signal from Bodipy-650 and its photocleavage. The same procedure was also performed by using dUTP-PC-ROX. The entire process was repeated five times by using the three fluorescent nucleotides to identify 7 bases in the DNA template. These results demonstrate that the PC nucleotide analogues can be incorporated accurately into a growing DNA strand during polymerase reaction on a chip, and the fluorophore can be detected and then efficiently cleaved using near-UV irradiation, thereby allowing the continuous identification of the template sequence.1,3-dipolar azide-alkyne cycloaddition ͉ DNA chip ͉ DNA sequencing by synthesis ͉ 2-nitrobenzyl linker ͉ photocleavage T he completion of the Human Genome Project has set the stage for screening genetic mutations to identify disease genes on a genome-wide scale (1). Accurate high-throughput methods for resequencing the intron͞exon regions of candidate genes are needed to explore the complete human genome sequence for disease-gene discovery. Recent studies also have demonstrated that an important route for identifying functional elements in the human genome is to sequence the genomes of many species that represent a wide sampling of the evolutionary tree (2). To overcome the limitations of the current sequencing technology based on electrophoresis using laser-induced fluorescence detection (3-5), a variety of new DNA-sequencing methods have been explored. Such techniques include pyrosequencing (6), MS sequencing (7-9), sequencing by hybridization (10), sequence-specific detection of singlestranded DNA using engineered nanopores (11), and sequencing of single DNA molecules (12) and polymerase colonies (13).Recently, new DNA-sequencing approaches based on sequencing by syn...

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mentioning

confidence: 99%

Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry

Seo

Bai

Ruparel

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

125

105

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“…It is distinct from sequencing by hybridization (SBH), which has been used successfully to characterize sequences de novo by hybridization to all n-mers or a well-chosen subset, typically in the range of 4-to 10-mers (Drmanac et al 1996(Drmanac et al , 1998Gunderson et al 1998;Brenner et al 2000). Our approach uses longer sequences, each designed to hybridize to a defined target with high specificity.…”

Section: Design Of Dna-based Decodingmentioning

confidence: 99%

Decoding Randomly Ordered DNA Arrays

Gunderson¹,

Kruglyak²,

Graige³

et al. 2004

Genome Res.

293

231

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We have developed a simple and efficient algorithm to identify each member of a large collection of DNA-linked objects through the use of hybridization, and have applied it to the manufacture of randomly assembled arrays of beads in wells. Once the algorithm has been used to determine the identity of each bead, the microarray can be used in a wide variety of applications, including single nucleotide polymorphism genotyping and gene expression profiling. The algorithm requires only a few labels and several sequential hybridizations to identify thousands of different DNA sequences with great accuracy. We have decoded tens of thousands of arrays, each with 1520 sequences represented at ∼30-fold redundancy by up to ∼50,000 beads, with a median error rate of <1 × 10 −4 per bead. The approach makes use of error checking codes and provides, for the first time, a direct functional quality control of every element of each array that is manufactured. The algorithm can be applied to any spatially fixed collection of objects or molecules that are associated with specific DNA sequences.Microarray technology, devised for the analysis of complex biological systems, uses the ability of a DNA strand to hybridize specifically to its complement to extract 1000s of measurements at a time from a single sample

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“…Thus, in principle, one could determine in a single microarray reaction the set of all k-long substrings of the target and try to infer the sequence from those data. The technique was validated in arrays of 7 and 8 mers (4,5), and up to 10 mers are possible with current array technology.…”

Section: S Equencing By Hybridization (Sbh) Was Invented In the Latementioning

confidence: 99%

A computational method for resequencing long DNA targets by universal oligonucleotide arrays

Pe’er

Arbili

Shamir

2002

Proc. Natl. Acad. Sci. U.S.A.

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Universal arrays contain all possible oligonucleotides of a certain length, typically 6 -10 bases. They can determine in a single experiment all substrings of that length that occur along a target sequence. That information, also called the spectrum of the sequence, is not sufficient to uniquely reconstruct a sequence longer than a few hundred bases. We have devised a polynomial algorithm that reconstructs the sequence, given the spectrum and an additional reference sequence, homologous to the target sequence. Such a reference is available, for example, in the identification of single-nucleotide polymorphisms. The algorithm can handle errors in the spectrum as well as substitutions, insertions, and deletions in the target sequence. We present extensive simulation results, which show that the algorithm correctly reconstructs target sequences of >2,000 nucleotides from error-prone 8-mer spectra when realistic levels of single-nucleotide polymorphisms are present.sequencing by hybridization ͉ mutation detection ͉ SNP genotyping ͉ hidden Markov models ͉ DNA microarrays Sequencing by HybridizationS equencing by hybridization (SBH) was invented in the late 1980s as an alternative to gel-based sequencing (1-3). This method makes use of a universal DNA microarray, which harbors all oligonucleotides of length k (called k-words, or simply words when k is clear). These oligonucleotides are hybridized to an unknown DNA fragment, whose sequence we would like to determine. Under ideal conditions, this target molecule would hybridize to all words whose Watson-Crick complements occur somewhere along its sequence. Thus, in principle, one could determine in a single microarray reaction the set of all k-long substrings of the target and try to infer the sequence from those data. The technique was validated in arrays of 7 and 8 mers (4, 5), and up to 10 mers are possible with current array technology.The fundamental computational problem in SBH is the reconstruction of a sequence from its spectrum, the set of all words occurring along the sequence. Pevzner (6) reduced that problem (assuming the number of occurrences of each word is known) to the polynomial task of finding an Eulerian path in a graph.The main weakness of SBH is ambiguous solutions: When several sequences have the same spectrum, there is no way to determine the true sequence. Theoretical analysis and simulations (4, 7) have shown that even when the spectrum is errorless and contains the multiplicity of each word, the average length of a uniquely reconstructible sequence using an 8-mer array is Ͻ200 bases, far below a single read length on a commercial gel-lane machine.Although an effective and competitive sequencing solution using SBH has yet to be demonstrated, this strategy continues to attract attention. In principle, SBH holds promise to considerably economize on the task of sequencing, one of the major efforts in modern biotechnology. Alternative array designs (8-10) as well as interactive protocols (11) were suggested. Similar Sequences Are UbiquitousSimilarity...

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Accurate sequencing by hybridization for DNA diagnostics and individual genomics

Cited by 151 publications

References 11 publications

Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry

Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry

Decoding Randomly Ordered DNA Arrays

A computational method for resequencing long DNA targets by universal oligonucleotide arrays

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