Research Progress of Probe Design Software of Oligonucleotide Microarrays_Journal of Biomedical Engineering

Authors：

CHENXi , WUZaoquan ,  LIUZhengchun

Department of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China;

Corresponding author：

LIUZhengchun, Email: liuzhengchunseu@126.com

Keywords：

microarray; oligonucleotide probes; probe design

DOI：

10.7507/1001-5515.20140041

Video：

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DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. Several sets of probe design software have been developed and are available to perform this work now. Every set of the software aims to different target sequences and shows different advantages and limitations. In this article, the research and development of these sets of software are reviewed in line with three main criteria, including specificity, sensitivity and melting temperature (T_m). In addition, based on the experimental results from literatures, these sets of software are classified according to their applications. This review will be helpful for users to choose an appropriate probe-design software. It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software.

Citation： CHENXi, WUZaoquan, LIUZhengchun. Research Progress of Probe Design Software of Oligonucleotide Microarrays. Journal of Biomedical Engineering, 2014, 31(1): 214-221. doi: 10.7507/1001-5515.20140041 Copy

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4.	GUDE L, BERKOVITCH S S, SANTOS W L, et al. Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays[J]. J Biol Chem, 2012, 287(22):18843-18853.
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8.	RINTA-KANTO J M, BVRGMANN H, GIFFORD S M, et al. Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray[J]. Environ Microbiol, 2011, 13(2):453-467.
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11.	CHIA-CHENG L, HSIN-YI L, CHIEN-YUN H, et al. DNA microarray analysis as a tool to investigate the therapeutic mechanisms and drug development of Chinese medicinal herbs[J]. Biomedicine, 2012, 2(1):10-16.
12.	ROBINSON J F, PENNINGS J L A, PIERSMA A H. A review of toxicogenomic approaches in developmental toxicology[M]. New Jersey:Humana Press, 2012:347-371.
13.	CANDELA M, CONSOLANDI C, SEVERGNINI M, et al. High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction--universal array approach[J]. BMC Microbiol, 2010, 10(1):116-131.
14.	WEI T, PEARSON M N, ARMSTRONG K, et al. Analysis of crucial factors resulting in microarray hybridization failure[J]. Mol Biosyst, 2012, 8(4):1325-1338.
15.	HOOYBERGHS J, VAN HUMMELEN P, CARLON E. The effects of mismatches on hybridization in DNA microarrays:determination of nearest neighbor parameters[J]. Nucleic Acids Res, 2009, 37(7):e53.
16.	AČU ESLOVAS V. Homology modeling[M]. New York:Humana Press, 2012:55-82.
17.	ÖZKUMURA E, AHNB S, AYCA Y, et al. Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches[J]. Biosens Bioelectron, 2010, 25(7):1789-1795.
18.	FLIBOTTE S, MOERMAN D G. Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization[J]. BMC Genomics, 2008, 9:497-508.
19.	LEMOINE S, COMBES F, LE CROM S. An evaluation of custom microarray applications:the oligonucleotide design challenge[J]. Nucleic Acids Res, 2009, 37(6):1726-1739.
20.	DUFOUR Y S, WESENBERG G E, TRITT A J, et al. ChipD:a web tool to design oligonucleotide probes for high-density tiling arrays[J]. Nucleic Acids Res, 2010, 38(Web Server issue):W321-W325.
21.	DUGAT-BONY E, MISSAOUI M, PEYRETAILLADE E, et al. HiSpOD:probe design for functional DNA microarrays[J]. Bioinformatics, 2011, 27(5):641-648.
22.	WANG X, SEED B. Selection of oligonucleotide probes for protein coding sequences[J]. Bioinformatics, 2003, 19(7):796-802.
23.	HUGUET J M, BIZARRO C V, FORNS N, et al. Single-molecule derivation of salt dependent base-pair free energies in DNA[J]. Proc Natl Acad Sci U S A, 2010, 107(35):15431-15436.
24.	DUMOUSSEAU M, RODRIGUEZ N, JUTY N, et al. MELTING, a fiexible platform to predict the melting temperatures of nucleic acids[J]. BMC Bioinformatics, 2012, 13(101):1471-2105.
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1. MATHEWS C K. Francis crick, hunter of life's secrets[J]. Biochemistry and Molecular Biology Education, 2011, 39(1):77-78.
2. JORDAN B. Microarrays in diagnostics and biomarker development[M]. Berlin:Springer Berlin Heidelberg, 2012:1-8.
3. PRICE J V, TANGSOMBATVISIT S, XU G, et al. On silico peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions[J]. Nat Med, 2012, 18(9):1434-1440.
4. GUDE L, BERKOVITCH S S, SANTOS W L, et al. Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays[J]. J Biol Chem, 2012, 287(22):18843-18853.
5. MA Z, GUO W, GUO X, et al. Modulation of behavioral phase changes of the migratory locust by the catecholamine metabolic pathway[J]. Proc Natl Acad Sci U S A, 2011, 108(10):3882-3887.
6. WANG Y, COTTMAN M, SCHIFFMAN J D. Molecular inversion probes:a novel microarray technology and its application in cancer research[J]. Cancer Genet, 2012, 205(7-8):341-355.
7. XU Y, DUANMU H, CHANG Z, et al. The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer[J]. Mol Biol Rep, 2012, 39(2):1627-1637.
8. RINTA-KANTO J M, BVRGMANN H, GIFFORD S M, et al. Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray[J]. Environ Microbiol, 2011, 13(2):453-467.
9. DELMONT T O, ROBE P, CECILLON S, et al. Accessing the soil metagenome for studies of microbial diversity[J]. Appl Environ Microbiol, 2011, 77(4):1315-1324.
10. DUC L, NEUENSCHWANDER S, REHRAUER H, et al. Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield[J]. Environ Microbiol, 2009, 11(8):2179-2189.
11. CHIA-CHENG L, HSIN-YI L, CHIEN-YUN H, et al. DNA microarray analysis as a tool to investigate the therapeutic mechanisms and drug development of Chinese medicinal herbs[J]. Biomedicine, 2012, 2(1):10-16.
12. ROBINSON J F, PENNINGS J L A, PIERSMA A H. A review of toxicogenomic approaches in developmental toxicology[M]. New Jersey:Humana Press, 2012:347-371.
13. CANDELA M, CONSOLANDI C, SEVERGNINI M, et al. High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction--universal array approach[J]. BMC Microbiol, 2010, 10(1):116-131.
14. WEI T, PEARSON M N, ARMSTRONG K, et al. Analysis of crucial factors resulting in microarray hybridization failure[J]. Mol Biosyst, 2012, 8(4):1325-1338.
15. HOOYBERGHS J, VAN HUMMELEN P, CARLON E. The effects of mismatches on hybridization in DNA microarrays:determination of nearest neighbor parameters[J]. Nucleic Acids Res, 2009, 37(7):e53.
16. AČU ESLOVAS V. Homology modeling[M]. New York:Humana Press, 2012:55-82.
17. ÖZKUMURA E, AHNB S, AYCA Y, et al. Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches[J]. Biosens Bioelectron, 2010, 25(7):1789-1795.
18. FLIBOTTE S, MOERMAN D G. Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization[J]. BMC Genomics, 2008, 9:497-508.
19. LEMOINE S, COMBES F, LE CROM S. An evaluation of custom microarray applications:the oligonucleotide design challenge[J]. Nucleic Acids Res, 2009, 37(6):1726-1739.
20. DUFOUR Y S, WESENBERG G E, TRITT A J, et al. ChipD:a web tool to design oligonucleotide probes for high-density tiling arrays[J]. Nucleic Acids Res, 2010, 38(Web Server issue):W321-W325.
21. DUGAT-BONY E, MISSAOUI M, PEYRETAILLADE E, et al. HiSpOD:probe design for functional DNA microarrays[J]. Bioinformatics, 2011, 27(5):641-648.
22. WANG X, SEED B. Selection of oligonucleotide probes for protein coding sequences[J]. Bioinformatics, 2003, 19(7):796-802.
23. HUGUET J M, BIZARRO C V, FORNS N, et al. Single-molecule derivation of salt dependent base-pair free energies in DNA[J]. Proc Natl Acad Sci U S A, 2010, 107(35):15431-15436.
24. DUMOUSSEAU M, RODRIGUEZ N, JUTY N, et al. MELTING, a fiexible platform to predict the melting temperatures of nucleic acids[J]. BMC Bioinformatics, 2012, 13(101):1471-2105.
25. MANN T, HUMBERT R, DORSCHNER M, et al. A thermodynamic approach to PCR primer design[J]. Nucleic Acids Res, 2009, 37(13):e95.
26. DUGAT-BONY E, PEYRETAILLADE E, PARISOT N, et al. Detecting unknown sequences with DNA microarrays:explorative probe design strategies[J]. Environ Microbiol, 2012, 14(2):356-371.

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