Development of a Physical Model-Based Algorithm for the Detection of Single-Nucleotide Substitutions by Using Tiling Microarrays

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Ono, Naoaki ^a   Suzuki, Shingo ^b   Furusawa, Chikara ^b   Shimizu, Hiroshi ^c   Yomo, Tetsuya ^c,d  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b RIKEN Center for Biosystems Dynamics Research   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ACCURACY; ARTICLE; BACTERIAL GENOME; BASE MISPAIRING; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; GENE SEQUENCE; GENETIC ALGORITHM; GENOME SIZE; NUCLEIC ACID BASE SUBSTITUTION; PHYSICAL MODEL; PROCESS DEVELOPMENT; THERMODYNAMICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POINT MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY;

EID: 84873820944     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054571     Document Type: Article

References (28)

1. Hacia J, Collins F, (1999) Mutational analysis using oligonucleotide microarrays. J Med Genet 36: 730-736.
2. Karaman M, Groshen S, Lee C, Pike B, Hacia J, (2005) Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays. Nucleic Acids Res 33: e33.
3. Zwick ME, Mcafee F, Cutler DJ, Read TD, Ravel J, et al. (2004) Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biology 6: R10.
4. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, et al. (2004) Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Research 14: 414-425.
5. Syvanen A, (2005) Toward genome-wide SNP genotyping. Nature Genetics 37: S5-S10.
6. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genetics 40: 1166-1174.
7. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, et al. (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311: 1932-1936.
8. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
9. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics 24: 133-141.
10. Alkan C, Coe BP, Eichler EE, (2011) Genome structural variation discovery and genotyping. Nature Reviews Genetics 12: 363-376.
11. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
12. Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, et al. (2003) Probe selection for high-density oligonucleotide arrays. Proceedings of the National Academy of Science. pp. 11237-11242.
13. Hekstra D, Taussig A, Magnasco M, Naef F, (2003) Absolute mrna concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res 31: 1962-1968.
14. Naef F, Magnasco M, (2003) Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys 68: 011906.
15. Wu C, Carta R, Zhang L, (2005) Sequence dependence of cross-hybridization on short oligo microarrays. Nucleic Acids Res 33: e84.
16. Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
17. Held GA, Grinstein G, Tu Y, (2003) Modeling of DNA microarray data by using physical properties of hybridization. Proceedings of the National Academy of Sciences of the United States of America 100: 7575-7580.
18. Zhang L, Miles M, Aldape K, (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol 21: 818-821.
19. Binder H, Preibisch S, Kirsten T, (2005) Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays. Langmuir 21: 9287-9302.
20. Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, et al. (2008) An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 24: 1278-1285.
21. Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T, (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS ONE 6: e19534.
22. Furusawa C, Ono N, Suzuki S, Agata T, Shimizu H, et al. (2009) Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. Bioinformatics 25: 36-41.
23. Unafold home page. Available: http://mfold.rna.albany.edu/. Accessed 2012 Jan 3.
24. Markham NR, Zuker M, (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33: W577-W581.
25. Markham NR, Zuker M, (2008) UNAFold: software for nucleic acid folding and hybridization. Methods in Mol Biol (Clifton, NJ) 453: 3-31.
26. R Development Core Team. Available: http://www.R-project.org. Accessed 2012 Jan 3.
27. The MUMmer home page. Available: http://mummer.sourceforge.net/. Accessed 2012 Jan 3.
28. Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.