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Radoje Drmanac,
Andrew B Sparks,
Matthew J Callow,
Aaron L Halpern,
Norman L Burns,
Bahram G Kermani,
Paolo Carnevali,
Igor Nazarenko,
Geoffrey B Nilsen,
George Yeung, [......],
Dylan Vu,
Alexander Wait Zaranek,
Xiaodi Wu, Snezana Drmanac,
Arnold R Oliphant,
William C Banyai,
Bruce Martin,
Dennis G Ballinger,
George M Church,
Clifford A Reid
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ABSTRACT: Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.
Science 11/2009; 327(5961):78-81. · 31.20 Impact Factor
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Radoje Drmanac, Snezana Drmanac,
Joerg Baier,
Gloria Chui,
Dan Coleman,
Robert Diaz,
Darryl Gietzen,
Aaron Hou,
Hui Jin,
Tatjana Ukrainczyk,
Chongjun Xu
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ABSTRACT: This chapter focuses on sequencing by hybridization (SBH), an advanced DNA sequencing technique first proposed in 1987 (1). SBH procedures determine DNA sequence information by screening DNA oligomers (typically 7-to 11-mers) for their ability
to hybridize with target DNA. The set of overlapping oligomers that matches the target DNA is then used to assemble its sequence.
The theory, practice, and history of SBH are reviewed in refs.
2 and 3.
02/2008: pages 173-179;
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ABSTRACT: By determining an organism’s DNA sequence, researchers can obtain critical information about its development and physiology,
its taxonomic relations, and its susceptibility to disease. There are three distinct methods of acquiring DNA sequence information:
sequence-specific DNA degradation, synthesis, and/or separation; sequence-specific DNA hybridization with oligonucleotide
probes; and nucleotide chain visualization. This chapter focuses on the second of these processes: the use of sequence-specific
hybridization of oligonucleotide probes of known sequence to determine primary DNA structure. Refined over the past decade,
such sequencing-by-hybridization (SBH) methods have become important tools in the field of genomics research.
02/2008: pages 39-51;
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09/2006; , ISBN: 9780470027318
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Michael Y Sha,
Ian D Walton,
Scott M Norton,
Micah Taylor,
Mark Yamanaka,
Michael J Natan,
Chongjun Xu, Snezana Drmanac,
Steve Huang,
Adam Borcherding,
Radoje Drmanac,
Sharron G Penn
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ABSTRACT: Single-nucleotide polymorphisms (SNP) are the most common form of sequence variation in the human genome. Large-scale studies demand high-throughput SNP genotyping platforms. Here we demonstrate the potential of encoded nanowires for use in a particles-based universal array for high-throughput SNP genotyping. The particles are encoded sub-micron metallic nanorods manufactured by electroplating inert metals such as gold and silver into templates and releasing the resulting striped nanoparticles. The power of this technology is that the particles are intrinsically encoded by virtue of the different reflectivity of adjacent metal stripes, enabling the generation of many thousands of unique encoded substrates. Using SNP found within the cytochrome P450 gene family, and a universal short oligonucleotide ligation strategy, we have demonstrated the simultaneous genotyping of 15 SNP; a format requiring discrimination of 30 encoded nanowires (one per allele). To demonstrate applicability to real-world applications, 160 genotypes were determined from multiplex PCR products from 20 genomic DNA samples.
Analytical and Bioanalytical Chemistry 03/2006; 384(3):658-66. · 3.78 Impact Factor
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ABSTRACT: Neurofibromatosis type 1 (NF1), one of the most common autosomal dominant disorders, is caused by mutations in the NF1 gene. A variety of methods are currently used in clinical settings to define disease-causing mutations. We describe microarray-based combinatorial sequencing-by-hybridization (cSBH), which overcomes some disadvantages associated with other techniques. Sequence readout of 2 kb was achieved on a single slide, with detection of base substitutions, insertions and small deletions. In addition, cSBH analysis of the entire NF1 gene demonstrates reproducibility, efficiency and reduced time; therefore, representing an alternative to extensive DNA sequence characterization.
Genetic Testing 02/2006; 10(1):8-17. · 1.17 Impact Factor
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ABSTRACT: Familial adenomatous polyposis (FAP) is an autosomal dominant inherited form of colorectal cancer, caused mostly by mutations in the APC gene. Due to the wide variety of mutations found and the large size of the APC gene, several methods of mutation detection are used, which can be time consuming and costly. Here we demonstrate a new method of mutation detection in the APC gene using an array-based approach termed combinatorial sequencing-by-hybridization (cSBH). In cSBH, a universal probe set is attached to a support and a second one is in solution. Two-probe ligation occurs when a DNA strand from the target PCR product consecutively anneals to both unlabeled array-bound and solution-phase dye-labeled probe, creating all target-complementary long-labeled probes attached to the surface. A standard array reader scores fluorescent signals at each array position. Cell lines and patient DNA with known APC gene mutations were analyzed using a cSBH-based HyChip trade mark product. Results show that this universal hexamer (6-mer) chip can successfully detect a range of mutations. Results are very robust for a continuous readout of 3.6 kb from a PCR target, with 99.97% accuracy on a single HyChip trade mark slide. cSBH is a fast, cost-efficient method for first stage mutation screening in the APC or any other gene.
Human Mutation 10/2004; 24(3):261-71. · 5.69 Impact Factor
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ABSTRACT: There is a rapidly developing need for new technologies to amplify millions of different targets from genomic DNA for high throughput genotyping and population gene-sequencing from diverse species. Here we describe a novel approach for the specific selection and amplification of genomic DNA fragments of interest that eliminates the need for costly and time consuming synthesis and testing of potentially millions of amplicon-specific primers. This technique relies upon Type IIs restriction enzyme digestion of genomic DNA and ligation of the fragments to double-sided adapters to form closed-circular DNA molecules. The novel use of double-sided adapters, assembled through the combinatorial use of two small universal sets of oligonucleotide building blocks, provides greater selection capacity by utilizing both sides of the adapter in a sequence-specific ligation event. As demonstrated, formation of circular structures results in protection of the desired molecules from nuclease treatment and enables a level of selectivity high enough to isolate single, or multiple, pre-defined fragments from the human genome when digested at over five million sites. Priming sites incorporated into the adapter allows the utilization of a common pair of primers for the amplification of any adapter-captured DNA fragment of interest.
Nucleic Acids Research 02/2004; 32(2):e21. · 8.03 Impact Factor
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Radoje Drmanac, Snezana Drmanac,
Gloria Chui,
Robert Diaz,
Aaron Hou,
Hui Jin,
Paul Jin,
Sunhee Kwon,
Scott Lacy,
Bill Moeur,
Jay Shafto,
Don Swanson,
Tatjana Ukrainczyk,
Chongjun Xu,
Deane Little
[show abstract]
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ABSTRACT: Efficient DNA sequencing of the genomes of individual species and organisms is a critical task for the advancement of biological sciences, medicine and agriculture. Advances in modern sequencing methods are needed to meet the challenge of sequencing such megabase to gigabase quantities of DNA. Two possible strategies for DNA sequencing exist: direct methods, in which each base position in the DNA chain is determined individually (e.g., gel sequencing or pyrosequencing), and indirect methods, in which the DNA sequence is assembled based on experimental determination of oligonucleotide content of the DNA chain. One promising indirect method is sequencing by hybridization (SBH), in which sets of oligonucleotides are hybridized under conditions that allow detection of complementary sequences in the target nucleic acid. The unprecedented sequence search parallelism of the SBH method has allowed development of high-throughput, low-cost, miniaturized sequencing processes on arrays of DNA samples or probes. Newly developed SBH methods use DNA ligation to combine relatively small sets of short probes to score potentially tens of millions of longer oligonucleotide sequences in a target DNA. Such combinatorial approaches allow analysis of DNA samples of up to several kilobases (several times longer than allowed by current direct methods) for a variety of DNA sequence analysis applications, including de novo sequencing, resequencing, mutation/SNP discovery and genotyping, and expression monitoring. Future advances in biochemistry and implementation of detection methods that allow single-molecule sensitivity may provide the necessary miniaturization, specificity, and multiplexing efficiency to allow routine whole genome analysis in a single solution-based hybridization experiment.
Advances in biochemical engineering/biotechnology 02/2002; 77:75-101. · 1.64 Impact Factor
