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Science 15 May 1998:
Vol. 280. no. 5366, pp. 1077 - 1082
DOI: 10.1126/science.280.5366.1077
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Reports

Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome

David G. Wang, Jian-Bing Fan, Chia-Jen Siao, Anthony Berno, Peter Young, Ron Sapolsky, Ghassan Ghandour, Nancy Perkins, Ellen Winchester, Jessica Spencer, Leonid Kruglyak, Lincoln Stein, Linda Hsie, Thodoros Topaloglou, Earl Hubbell, Elizabeth Robinson, Michael Mittmann, Macdonald S. Morris, Naiping Shen, Dan Kilburn, John Rioux, Chad Nusbaum, Steve Rozen, Thomas J. Hudson, Robert Lipshutz, * Mark Chee, Eric S. Lander *

Single-nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, and they provide powerful tools for a variety of medical genetic studies. In a large-scale survey for SNPs, 2.3 megabases of human genomic DNA was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips. A total of 3241 candidate SNPs were identified. A genetic map was constructed showing the location of 2227 of these SNPs. Prototype genotyping chips were developed that allow simultaneous genotyping of 500 SNPs. The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs.

D. G. Wang, C.-J. Siao, P. Young, N. Perkins, E. Winchester, J. Spencer, L. Kruglyak, L. Stein, E. Robinson, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
J.-B. Fan, A. Berno, R. Sapolsky, G. Ghandour, L. Hsie, T. Topaloglou, E. Hubbell, M. Mittmann, M. S. Morris, N. Shen, R. Lipshutz, M. Chee, Affymetrix, Incorporated, 3380 Central Expressway, Santa Clara, CA 95051, USA.
E. S. Lander, Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
*   To whom correspondence should be addressed.

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A computational method for resequencing long DNA targets by universal oligonucleotide arrays.
I. Pe'er, N. Arbili, and R. Shamir (2002)
PNAS 99, 15492-15496
   Abstract »    Full Text »    PDF »
Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia.
I. Chumakov, M. Blumenfeld, O. Guerassimenko, L. Cavarec, M. Palicio, H. Abderrahim, L. Bougueleret, C. Barry, H. Tanaka, P. La Rosa, et al. (2002)
PNAS 99, 13675-13680
   Abstract »    Full Text »    PDF »
Matrix Metalloproteinase-1 and Matrix Metalloproteinase-3 Gene Promoter Polymorphisms Are Associated With Carotid Artery Stenosis.
G. Ghilardi, M. L. Biondi, M. DeMonti, O. Turri, E. Guagnellini, and R. Scorza (2002)
Stroke 33, 2408-2412
   Abstract »    Full Text »    PDF »
Single-Nucleotide Polymorphism Allele Frequencies Determined by Quantitative Kinetic Assay of Pooled DNA.
K. Xu, R. H. Lipsky, W. Mangal, E. Ferro, and D. Goldman (2002)
Clin. Chem. 48, 1605-1608
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A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides.
J. L. Wolfe, T. Kawate, D. A. Sarracino, M. Zillmann, J. Olson, V. P. Stanton Jr., and G. L. Verdine (2002)
PNAS 99, 11073-11078
   Abstract »    Full Text »    PDF »
Single nucleotide polymorphism seeking long term association with complex disease.
B. W. Kirk, M. Feinsod, R. Favis, R. M. Kliman, and F. Barany (2002)
Nucleic Acids Res. 30, 3295-3311
   Abstract »    Full Text »    PDF »
Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array.
R. McKendry, J. Zhang, Y. Arntz, T. Strunz, M. Hegner, H. P. Lang, M. K. Baller, U. Certa, E. Meyer, H.-J. Guntherodt, et al. (2002)
PNAS 99, 9783-9788
   Abstract »    Full Text »    PDF »
Parallel Characterization of Anaerobic Toluene- and Ethylbenzene-Degrading Microbial Consortia by PCR-Denaturing Gradient Gel Electrophoresis, RNA-DNA Membrane Hybridization, and DNA Microarray Technology.
Y. Koizumi, J. J. Kelly, T. Nakagawa, H. Urakawa, S. El-Fantroussi, S. Al-Muzaini, M. Fukui, Y. Urushigawa, and D. A. Stahl (2002)
Appl. Envir. Microbiol. 68, 3215-3225
   Abstract »    Full Text »    PDF »
Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences.
L. Y.Y. Chen, S.-H. Lu, E. S.C. Shih, and M.-J. Hwang (2002)
Genome Res. 12, 1106-1111
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Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA).
Y. Eitan and Y. Kashi (2002)
Nucleic Acids Res. 30, e62
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Mapping QTLs Regulating Morpho-physiological Traits and Yield: Case Studies, Shortcomings and Perspectives in Drought-stressed Maize.
R. TUBEROSA, S. SALVI, M. C. SANGUINETI, P. LANDI, M. MACCAFERRI, and S. CONTI (2002)
Ann. Bot. 89, 941-963
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Hormonal Genomics.
C. P. Leo, S. Y. Hsu, and A. J. W. Hsueh (2002)
Endocr. Rev. 23, 369-381
   Abstract »    Full Text »    PDF »


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