Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 4, 2010, Pages 1482-1487

  Gresham, David ^a,b   Curry, Bo ^c   Ward, Alexandra ^a   Gordon, D Benjamin ^c   Brizuela, Leonardo ^c   Kruglyak, Leonid ^a   Botstein, David ^a  

^a PRINCETON UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c AGILENT TECHNOLOGIES   (United States)

Author keywords

DNA DNA hybridization; Melting temperature; Probe design; Sequence discrimination; Single nucleotide polymorphisms

Indexed keywords

DNA;

ARTICLE; DNA MICROARRAY; DNA SEQUENCE; FUNGAL STRAIN; GENE EXPRESSION; GENE MUTATION; GENE TECHNOLOGY; GENOME; GENOTYPE; HETEROZYGOSITY; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; DNA PROBES; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

SACCHAROMYCES CEREVISIAE;

EID: 76549129029     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0913883107     Document Type: Article

References (29)

1. Gresham D, Dunham MJ, Botstein D (2008) Comparing whole genomes using DNA microarrays. Nat Rev Genet 9:291-302.
2. Lipshutz RJ, et al. (1995) Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19:442-447.
3. Winzeler EA, et al. (1998) Direct allelic variation scanning of the yeast genome. Science 281:1194-1197.
4. Gresham D, et al. (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311:1932-1936.
5. Albert TJ, et al. (2005) Mutation discovery in bacterial genomes: Metronidazole resistance in Helicobacter pylori. Nat Methods 2:951-953.
6. Wong CW, et al. (2004) Tracking the evolution of the SARS coronavirus using highthroughput, high-density resequencing arrays. Genome Res 14:398-405.
7. Gagneur J, et al. (2009) Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol 5:274.
8. Borevitz JO, et al. (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13:513-523.
9. Segrè AV, Murray AW, Leu JY (2006) High-resolution mutation mapping reveals parallel experimental evolution in yeast. PLoS Biol 4:e256.
10. Brauer MJ, Christianson CM, Pai DA, Dunham MJ (2006) Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics 173: 1813-1816.
11. Hu G, Llinás M, Li J, Preiser PR, Bozdech Z (2007) Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 8:350.
12. Xu Q, Schlabach MR, Hannon GJ, Elledge SJ (2009) Design of 240,000 orthogonal 25mer DNA barcode probes. Proc Natl Acad Sci USA 106:2289-2294.
13. Alemayehu S, et al. (2009) Influence of buffer species on the thermodynamics of short DNA duplex melting: Sodium phosphate versus sodium cacodylate. J Phys Chem B 113:2578-2586.
14. Fish DJ, et al. (2007) DNA multiplex hybridization on microarrays and thermodynamic stability in solution: A direct comparison. Nucleic Acids Res 35:7197-7208.
15. Fish DJ, Horne MT, Searles RP, Brewood GP, Benight AS (2007) Multiplex SNP discrimination. Biophys J 92:L89-L91.
16. Horne MT, Fish DJ, Benight AS (2006) Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions. Biophys J 91:4133-4153.
17. SantaLucia J, Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460-1465.
18. SantaLucia J, Jr, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555-3562.
19. SantaLucia J, Jr, Hicks D (2004) The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct 33:415-440.
20. Ronald J, et al. (2005) Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res 15: 284-291.
21. Herring CD, et al. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38: 1406-1412.
22. Tan JC, et al. (2009) Optimizing comparative genomic hybridization probes for genotyping and SNP detection in Plasmodium falciparum. Genomics 93:543-550.
23. Herring CD, Palsson B∅ (2007) An evaluation of comparative genome sequencing (CGS) by comparing two previously-sequenced bacterial genomes. BMC Genomics 8: 274.
24. Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458:342-345.
25. Gresham D, et al. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet 4:e1000303.
26. Ho CH, et al. (2009) A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol 27:369-377.
27. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454:479-485.
28. Kahvejian A, Quackenbush J, Thompson JF (2008) What would you do if you could sequence everything? Nat Biotechnol 26:1125-1133.
29. Shendure J (2008) The beginning of the end for microarrays? Nat Methods 5:585-587.