Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/wiley/automation-in-genotyping-of-single-nucleotide-polymorphisms-5FsBTPwn5i
References (85)
-
Darren Day, Phyllis Speiser, Perrin White, Francis Barany (1995)
Detection of steroid 21-hydroxylase alleles using gene-specific PCR and a multiplexed ligation detection reaction.Genomics, 29 1
-
Xiangning Chen, Barbara Zehnbauer, Andreas Gnirke, Pui-Yan Kwok (1997)
Fluorescence energy transfer detection as a homogeneous DNA diagnostic method.Proceedings of the National Academy of Sciences of the United States of America, 94 20
-
Rui Mei, P. Galipeau, Cynthia Prass, A. Berno, G. Ghandour, Nila Patil, Roger Wolff, Mark Chee, Brian Reid, David Lockhart (2000)
Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays.Genome research, 10 8
-
Eric Lander (1999)
Array of hopeNature Genetics, 21 Suppl 1
-
M. Shchepinov, R. Chalk, E. Southern (1999)
Trityl mass-tags for encoding in combinatorial oligonucleotide synthesis.Nucleic acids symposium series, 42
-
B. Parsons, R. Heflich (1997)
Genotypic selection methods for the direct analysis of point mutations.Mutation research, 387 2
-
H. Baron, S. Fung, A. Aydın, S. Bähring, F. Luft, H. Schuster (1996)
Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemiaNature Biotechnology, 14
-
John Harrington, Michael Lieber (1994)
Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair.Genes & development, 8 11
-
Jingwen Chen, Marie Iannone, May-Sung Li, J. Taylor, Philip Rivers, Anita Nelsen, Kimberly Slentz-Kesler, Allen Roses, Michael Weiner (2000)
A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension.Genome research, 10 4
-
Rolfe Anderson, X. Su, G. Bogdan, Jeffery Fenton (2000)
A miniature integrated device for automated multistep genetic assays.Nucleic acids research, 28 12
-
J. Shumaker, A. Metspalu, C. Caskey (1996)
Mutation detection by solid phase primer extensionHuman Mutation, 7
-
B. Healey, R. Matson, D. Walt (1997)
Fiberoptic DNA sensor array capable of detecting point mutations.Analytical biochemistry, 251 2
-
Olga Kalinina, Irina Lebedeva, James Brown, Jonathan Silver (1997)
Nanoliter scale PCR with TaqMan detection.Nucleic acids research, 25 10
-
D. Little, A. Braun, B. Darnhofer-Demar, A. Frilling, Yunzhi Li, Robert Jr., H. Köster (1997)
Detection of RET proto-oncogene codon 634 mutations using mass spectrometryJournal of Molecular Medicine, 75
-
R. Sosnowski, E. Tu, W. Butler, J. O'connell, M. Heller (1997)
Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control.Proceedings of the National Academy of Sciences of the United States of America, 94 4
-
Christine Debouck, P. Goodfellow (1999)
DNA microarrays in drug discovery and developmentNature Genetics, 21 Suppl 1
-
Marie Iannone, J. Taylor, Jingwen Chen, May-Sung Li, Philip Rivers, Kimberly Slentz-Kesler, Michael Weiner (2000)
Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry.Cytometry, 39 2
-
T. Pastinen, A. Kurg, A. Metspalu, L. Peltonen, A. Syvänen (1997)
Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays.Genome research, 7 6
-
D. Mccormick (1986)
Sequence the Human GenomeBio/Technology, 4
-
Paul Grossman, Will Bloch, Eleanor Brinson, Conway Chang, Faye Eggerding, Steven Fung, David lovannisci, Sam Woo, E. Winn-Deen (1994)
High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation.Nucleic acids research, 22 21
-
A. Syvänen (1999)
From gels to chips: “Minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphismsHuman Mutation, 13
-
Sanjay Tyagi, D. Bratu, F. Kramer (1998)
Multicolor molecular beacons for allele discriminationNature Biotechnology, 16
-
A. Syvänen, A. Sajantila, M. Lukka (1993)
Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing.American journal of human genetics, 52 1
-
Xiangning Chen, K. Livak, Pui-Yan Kwok (1998)
A homogeneous, ligase-mediated DNA diagnostic test.Genome research, 8 5
-
M. Ronaghi, M. Nygren, J. Lundeberg, P. Nyrén (1999)
Analyses of secondary structures in DNA by pyrosequencing.Analytical biochemistry, 267 1
-
Xiangning Chen, Pui-Yan Kwok (1997)
Template-directed dye-terminator incorporation (TDI) assay: a homogeneous DNA diagnostic method based on fluorescence resonance energy transfer.Nucleic acids research, 25 2
-
M. Khanna, P. Park, M. Zirvi, W. Cao, A. Picon, J. Day, P. Paty, F. Barany (1999)
Multiplex PCR/LDR for detection of K-ras mutations in primary colon tumorsOncogene, 18
-
L. Defrancesco (1998)
TELOMERE WITHOUT END, AMEN : LOOKING INTO LONGEVITY WITH TELOMERE DETECTION KITSThe Scientist, 12
-
A. Pease, D. Solas, E. Sullivan, M. Cronin, C. Holmes, S. Fodor (1994)
Light-generated oligonucleotide arrays for rapid DNA sequence analysis.Proceedings of the National Academy of Sciences of the United States of America, 91 11
-
T. Pastinen, J. Partanen, A. Syvänen (1996)
Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation.Clinical chemistry, 42 9
-
D. Schmalzing, A. Belenky, M. Novotny, L. Koutny, O. Salas‐Solano, S. El-Difrawy, A. Adourian, P. Matsudaira, D. Ehrlich (2000)
Microchip electrophoresis: a method for high-speed SNP detection.Nucleic acids research, 28 9
-
M. Ronaghi, S. Karamohamed, B. Pettersson, M. Uhlén, P. Nyrén (1996)
Real-time DNA sequencing using detection of pyrophosphate release.Analytical biochemistry, 242 1
-
U. Landegren, M. Nilsson, Pui-Yan Kwok (1998)
Reading bits of genetic information: methods for single-nucleotide polymorphism analysis.Genome research, 8 8
-
A. Brookes, P. Kwok, P. White, P. Oefner (2001)
SNiPpets from the Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis, September 8–11, 2000, Taos, New Mexico, USAHuman Mutation, 17
-
H. Pang, E. Yeung (2000)
Automated one-step DNA sequencing based on nanoliter reaction volumes and capillary electrophoresis.Nucleic acids research, 28 15
-
D. Shalon, S. Smith, P. Brown (1996)
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.Genome research, 6 7
-
A. Syvänen (1994)
Detection of point mutations in human genes by the solid-phase minisequencing method.Clinica chimica acta; international journal of clinical chemistry, 226 2
-
G. Ramsay (1998)
DNA chips: State-of-the artNature Biotechnology, 16
-
Sanjay Tyagi, F. Kramer (1996)
Molecular Beacons: Probes that Fluoresce upon HybridizationNature Biotechnology, 14
-
Jian-Bing Fan, Xiaoqiong Chen, M. Halushka, A. Berno, Xiaohua Huang, Tom Ryder, R. Lipshutz, D. Lockhart, A. Chakravarti (2000)
Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays.Genome research, 10 6
-
I. Day, S. Humphries (1994)
Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose.Analytical biochemistry, 222 2
-
Chen (1999)
492Genome Res, 9
-
W. Pusch, K. Kraeuter, T. Froehlich, Y. Stalgies, M. Kostrzewa (2001)
Genotools SNP manager: a new software for automated high-throughput MALDI-TOF mass spectrometry SNP genotyping.BioTechniques, 30 1
-
Martina Samiotaki, M. Kwiatkowski, J. Parik, U. Landegren (1994)
Dual-color detection of DNA sequence variants by ligase-mediated analysis.Genomics, 20 2
-
Brown (1999)
33Nat Genet, 21
-
M. Nilsson, K. Krejčí, J. Koch, M. Kwiatkowski, P. Gustavsson, U. Landegren (1997)
Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21Nature Genetics, 16
-
R. Lipshutz, S. Fodor, T. Gingeras, D. Lockhart (1999)
High density synthetic oligonucleotide arraysNature Genetics, 21 Suppl 1
-
(2000)
Keynote lecture at the Cold Spring Harbor meeting of genome sequencing and biology -
L. Kruglyak (1997)
The use of a genetic map of biallelic markers in linkage studiesNature Genetics, 17
-
L. Haff, I. Smirnov (1997)
Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry.Genome research, 7 4
-
P. Ross, L. Hall, I. Smirnov, L. Haff (1998)
High level multiplex genotyping by MALDI-TOF mass spectrometryNature Biotechnology, 16
-
D. Meldrum (2000)
Automation for genomics, part two: sequencers, microarrays, and future trends.Genome research, 10 9
-
D. Ryan, Bonnie Nuccie, D. Arvan (1999)
Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay.Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology, 4 2
-
T. Pastinen, M. Raitio, K. Lindroos, Päivi Tainola, L. Peltonen, A. Syvänen (2000)
A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays.Genome research, 10 7
-
P. Kwok (1998)
Genotyping by mass spectrometry takes flightNature Biotechnology, 16
-
Sascha Sauer, D. Lechner, Kurt Berlin, Christine Plançon, A. Heuermann, Hans Lehrach, Ivo Gut (2000)
Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay.Nucleic acids research, 28 23
-
C. Newton, A. Graham, L. Heptinstall, S. Powell, C. Summers, N. Kalsheker, J. Smith, A. Markham (1989)
Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS).Nucleic acids research, 17 7
-
V. Cheung, M. Morley, Francisco Aguilar, A. Massimi, R. Kucherlapati, G. Childs (1999)
Making and reading microarraysNature Genetics, 21 Suppl 1
-
David Wang, Jian-Bing Fan, C. Siao, A. Berno, Peter Young, R. Sapolsky, G. Ghandour, Nancy Perkins, E. Winchester, Jessica Spencer, L. Kruglyak, Lincoln Stein, L. Hsie, T. Topaloglou, E. Hubbell, Elizabeth Robinson, Mike Mittmann, M. Morris, Naiping Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. Hudson, R. Lipshutz, M. Chee, E. Lander (1998)
Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.Science, 280 5366
-
T. Griffin, Jeff Hall, J. Prudent, L. Smith (1999)
Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America, 96 11
-
H. Crollius, O. Jaillon, A. Bernot, C. Dasilva, L. Bouneau, Cécile Fischer, C. Fizames, P. Wincker, P. Brottier, F. Quétier, W. Saurin, J. Weissenbach (2000)
Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequenceNature Genetics, 25
-
L. Kruglyak (1999)
Prospects for whole-genome linkage disequilibrium mapping of common disease genesNature Genetics, 22
-
John Butler, P. Jiang-Baucom, Meng Huang, Phillip Belgrader, James Girard (1996)
Peptide nucleic acid characterization by MALDI-TOF mass spectrometry.Analytical chemistry, 68 18
-
S. Germer, M. Holland, Russell Higuchi (2000)
High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR.Genome research, 10 2
-
A. Shuber, L. Michalowsky, G. Nass, J. Skoletsky, L. Hire, S. Kotsopoulos, M. Phipps, D. Barberio, K. Klinger (1997)
High throughput parallel analysis of hundreds of patient samples for more than 100 mutations in multiple disease genes.Human molecular genetics, 6 3
-
K. Livak, Jeffrey Marmaro, J. Todd (1995)
Towards fully automated genome–wide polymorphism screeningNature Genetics, 9
-
M. Shi, M. Bleavins, F. Iglesia (1999)
Technologies for detecting genetic polymorphisms in pharmacogenomics.Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology, 4 4
-
E. Maier, H. Lehrach (1997)
Neue Techniken zur Automatisierung in der DNA-SequenzierungChemie in Unserer Zeit, 31
-
P. Ross, L. Hall, L. Haff (2000)
Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry.BioTechniques, 29 3
-
C. Mein, B. Barratt, M. Dunn, Thorsten Siegmund, Annabel Smith, L. Esposito, S. Nutland, H. Stevens, A. Wilson, M. Phillips, Nancy Jarvis, Scott Law, Monika Arruda, J. Todd (2000)
Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation.Genome research, 10 3
-
T. Griffin, Wei-Ying Tang, Lloyd Smith (1997)
Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometryNature Biotechnology, 15
-
H. Cai, P. White, D. Torney, A. Deshpande, Z. Wang, R. Keller, B. Marrone, J. Nolan (2000)
Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring.Genomics, 66 2
-
International Consortium (2001)
Initial sequencing and analysis of the human genomeNature, 409
-
Pamela Holland, R. Abramson, R. Watson, D. Gelfand (1991)
Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America, 88
-
Xiangning Chen, L. Levine, Pui-Yan Kwok (1999)
Fluorescence polarization in homogeneous nucleic acid analysis.Genome research, 9 5
-
L. Francesco (1998)
THE NEXT NEW WAVE IN GENOME ANALYSIS: INVADER ASSAYS DEVELOPED BY THIRD WAVE TECHNOLOGIES, INC.The Scientist, 12
-
D. Meldrum (2000)
Automation for genomics, part one: preparation for sequencing.Genome research, 10 8
-
M. Nilsson, H. Malmgren, M. Samiotaki, M. Kwiatkowski, B. Chowdhary, U. Landegren (1994)
Padlock probes: circularizing oligonucleotides for localized DNA detection.Science, 265 5181
-
S. Sauer, D. Lechner, K. Berlin, H. Lehrach, J. Escary, Nick Fox, Ivo Gut (2000)
A novel procedure for efficient genotyping of single nucleotide polymorphisms.Nucleic acids research, 28 5
-
F. Barany (1991)
Genetic disease detection and DNA amplification using cloned thermostable ligase.Proceedings of the National Academy of Sciences of the United States of America, 88 1
-
Jia Li, J. Butler, Yuping Tan, Hua Lin, Stephanie Royer, L. Ohler, T. Shaler, J. Hunter, D. Pollart, J. Monforte, Christopher Becker (1999)
Single nucleotide polymorphism determination using primer extension and time‐of‐flight mass spectrometryELECTROPHORESIS, 20
-
M. Egholm, O. Buchardt, L. Christensen, C. Behrens, S. Freier, D. Driver, R. Berg, Seog Kim, B. Nordén, P. Nielsen (1993)
PNA hybridizes to complementary oligonucleotides obeying the WatsonCrick hydrogen-bonding rulesNature, 365
-
J. McCarthy, R. Hilfiker (2000)
The use of single-nucleotide polymorphism maps in pharmacogenomicsNature Biotechnology, 18
-
C. Edman, D. Raymond, David Wu, E. Tu, R. Sosnowski, W. Butler, Michael Nerenberg, M. Heller (1997)
Electric field directed nucleic acid hybridization on microchips.Nucleic acids research, 25 24
-
Landegren, Samiotaki, Nilsson, Malmgren, Kwiatkowski (1996)
Detecting Genes with LigasesMethods, 9 1
- Publisher
- Wiley
- Copyright
- Copyright © 2001 Wiley Subscription Services, Inc., A Wiley Company
- ISSN
- 1059-7794
- eISSN
- 1098-1004
- DOI
- 10.1002/humu.1131
- pmid
- 11385706
- Publisher site
- See Article on Publisher Site
Abstract
Automation for genotyping of single nucleotide polymorphisms (SNPs) can be split into the automation of the sample preparation and the automation of the analysis technology. SNP genotyping methods are reviewed and solutions for their automation discussed. A panacea for SNP genotyping does not exist. Different scientific questions require adapted solutions. The choice of a technology for SNP genotyping depends on whether few different SNPs are to be genotyped in many individuals, or many different SNPs are to be genotyped in few individuals. The requirements of throughput and the ease of establishing an SNP genotyping operation are important, as well as the degree of integration. The potential and state‐of‐the‐art of different solutions are outlined. Hum Mutat 17:475–492, 2001. © 2001 Wiley‐Liss, Inc.
Journal
Human Mutation – Wiley
Published: Jun 1, 2001
Keywords: SNP; automation; genotyping; DNA analysis; mutation detection; variation; robotics; arrays; microarrays; microspheres; mass spectrometry