Related Content
Search Google Scholar for:
|
Published Online March 9, 2006 Science
DOI: 10.1126/science.1123726
|
|
Reports
Submitted on December 12, 2005
Accepted on February 24, 2006
Genome-wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA Microarray
David Gresham 1*,
Douglas M. Ruderfer 2,
Stephen C. Pratt 2,
Joseph Schacherer 2,
Maitreya Dunham 3,
David Botstein 1,
Leonid Kruglyak 2*
1 Lewis-Sigler Institute for Integrative Genomics; Department of Molecular Biology
2 Lewis-Sigler Institute for Integrative Genomics; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
3 Lewis-Sigler Institute for Integrative Genomics
* To whom correspondence should be addressed.
David Gresham , E-mail: dgresham{at}genomics.princeton.edu Leonid Kruglyak , E-mail: leonid{at}genomics.princeton.edu
A central challenge of genomics is to detect, simply and inexpensively, all differences in sequence among the genomes of individual members of a species. We devised a system to detect all single-nucleotide differences between genomes using data from a single hybridization to a whole genome DNA microarray. This allowed us to detect a variety of spontaneous single base-pair substitutions, insertions and deletions, and most (>90%) of the 30,000 known single-nucleotide polymorphisms between two Saccharomyces cerevisiae strains. We applied this approach to elucidate the genetic basis of phenotypic variants and identify the small number of single base-pair changes accumulated during experimental evolution of yeast.
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
- Eco1-Dependent Cohesin Acetylation During Establishment of Sister Chromatid Cohesion.
- T. R. Ben-Shahar, S. Heeger, C. Lehane, P. East, H. Flynn, M. Skehel, and F. Uhlmann (2008)
Science
321, 563-566
| Abstract »
| Full Text »
| PDF »
- Comparative Genomics of "Dehalococcoides ethenogenes" 195 and an Enrichment Culture Containing Unsequenced "Dehalococcoides" Strains.
- K. A. West, D. R. Johnson, P. Hu, T. Z. DeSantis, E. L. Brodie, P. K. H. Lee, H. Feil, G. L. Andersen, S. H. Zinder, and L. Alvarez-Cohen (2008)
Appl. Envir. Microbiol.
74, 3533-3540
| Abstract »
| Full Text »
| PDF »
- Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis.
- Z. He and J. Zhou (2008)
Appl. Envir. Microbiol.
74, 2957-2966
| Abstract »
| Full Text »
| PDF »
- Influence of genotype and nutrition on survival and metabolism of starving yeast.
- V. M. Boer, S. Amini, and D. Botstein (2008)
PNAS
105, 6930-6935
| Abstract »
| Full Text »
| PDF »
- Genomic Analysis of Adaptive Differentiation in Drosophila melanogaster.
- T. L. Turner, M. T. Levine, M. L. Eckert, and D. J. Begun (2008)
Genetics
179, 455-473
| Abstract »
| Full Text »
| PDF »
- Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle.
- I. J. Tsai, D. Bensasson, A. Burt, and V. Koufopanou (2008)
PNAS
105, 4957-4962
| Abstract »
| Full Text »
| PDF »
- Detecting genetic variation in microarray expression data.
- J. A. Greenhall, M. A. Zapala, M. Caceres, O. Libiger, C. Barlow, N. J. Schork, and D. J. Lockhart (2007)
Genome Res.
17, 1228-1235
| Abstract »
| Full Text »
| PDF »
- Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.
- W. Wei, J. H. McCusker, R. W. Hyman, T. Jones, Y. Ning, Z. Cao, Z. Gu, D. Bruno, M. Miranda, M. Nguyen, et al. (2007)
PNAS
104, 12825-12830
| Abstract »
| Full Text »
| PDF »
- Genome-wide identification of spliced introns using a tiling microarray.
- Z. Zhang, J. R. Hesselberth, and S. Fields (2007)
Genome Res.
17, 503-509
| Abstract »
| Full Text »
| PDF »
- Synthetic ecology: A model system for cooperation.
- M. J. Dunham (2007)
PNAS
104, 1741-1742
| Full Text »
| PDF »
- Genetic interaction screens advance in reverse.
- S. Komili and F. P. Roth (2007)
Genes & Dev.
21, 137-142
| Full Text »
| PDF »
- Transcript mapping with high-density oligonucleotide tiling arrays.
- W. Huber, J. Toedling, and L. M. Steinmetz (2006)
Bioinformatics
22, 1963-1970
| Abstract »
| Full Text »
| PDF »
- Mapping Novel Traits by Array-Assisted Bulk Segregant Analysis in Saccharomyces cerevisiae.
- M. J. Brauer, C. M. Christianson, D. A. Pai, and M. J. Dunham (2006)
Genetics
173, 1813-1816
| Abstract »
| Full Text »
| PDF »
|
|