Coupling an universal primer to SBE combined spectral codification strategy for single nucleotide polymorphism analysis

Journal of Biotechnology

Volumn 168, Issue 1, 2013, Pages 90-94

  Cordeiro, Mílton ^a   Giestas, Letícia ^a   Lima, João C ^a   Baptista, Pedro ^a  

^a UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

FRET; SBE; SNP; Spectral codification; Universal SBE primer

Indexed keywords

FRET; SBE; SNP; SPECTRAL CODIFICATION; UNIVERSAL SBE PRIMER;

ENERGY TRANSFER; OLIGONUCLEOTIDES;

GENES;

DIDEOXYNUCLEOTIDE; OLIGONUCLEOTIDE;

ALLELE; ARTICLE; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENCE SPECTROSCOPY; GENE LOCUS; GENETIC PROCEDURES; GENETIC VARIABILITY; HUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; SINGLE BASE EXTENSION; SINGLE NUCLEOTIDE POLYMORPHISM;

FRET; SBE; SNP; SPECTRAL CODIFICATION; UNIVERSAL SBE PRIMER;

DNA PRIMERS; FLUORESCENCE RESONANCE ENERGY TRANSFER; MODELS, BIOLOGICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84883776215     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.08.005     Document Type: Article

References (20)

1. Beuselinck B., Karadimou A., Lambrechts D., Claes B., Wolter P., Couchy G., Berkers J., Paridaens R., Schöffski P., Méjean A., Verkarre V., Lerut E., de la Taille A., Tourani J.-M., Bigot P., Linassier C., Négrier S., Berger J., Patard J.-J., Zucman-Rossi J., Oudard S. Single-nucleotide polymorphisms associated with outcome in metastatic renal cell carcinoma treated with sunitinib. Br. J. Cancer 2013, 108:887-900. 10.1038/bjc.2012.548.
2. Bogus M., Sobrino B., Bender K., Carracedo A., Schneider P. Rapid microarray-based typing of forensic SNPs. Int. Cong. Ser. 2006, 1288:37-39. 10.1016/j.ics.2005.10.017.
3. Chen X., Kwok P. Template-directed dye-terminator incorporation (TDI) assay: a homogeneous DNA diagnostic method based on fluorescence resonance energy transfer. Nucleic Acids Res. 1997, 25:347-353. 10.1093/nar/25.2.347.
4. Dieffenbach C.W., Lowe T.M., Dveksler G.S. General concepts for PCR primer design. Genome Res. 1993, 3:S30-S37.
5. Frayling T., Timpson N., Weedon M., Zeggini E., Freathy R., Lindgren C., Perry J., Elliott K., Lango H., Rayner N., Shields B., Harries L., Barrett J., Ellard S., Groves C., Knight B., Patch A.-M., Ness A., Ebrahim S., Lawlor D., Ring S., Ben-Shlomo Y., Jarvelin M.-R., Sovio U., Bennett A., Melzer D., Ferrucci L., Loos R., Barroso I., Wareham N., Karpe F., Owen K., Cardon L., Walker M., Hitman G., Palmer C., Doney A., Morris A., Smith G., Hattersley A., McCarthy M. A Common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 2007, 316:889-894. 10.1126/science.1141634.
6. Freeman B., Buchman T., McGrath S., Tabrizi A., Zehnbauer B. Template-directed dye-terminator incorporation with fluorescence polarization detection for analysis of single nucleotide polymorphisms implicated in sepsis. J. Mol. Diagn. 2002, 4:209-215. 10.1016/S1525-1578(10)60705-2.
7. Giestas L., Ferreira G., Baptista P., Lima J. Multiplexed spectral coding for simultaneous detection of DNA hybridization reactions based on FRET. Sens. Actuators B 2008, 134:146-157. 10.1016/j.snb.2008.04.038.
8. Giestas L., Petrov V., Baptista P., Lima J. General FRET-based coding for application in multiplexing methods. Photochem. Photobiol. Sci. 2009, 8:1130-1138. 10.1039/b906033b.
9. Giestas L., Lima J., Baptista P. Coupling single base extension to a spectral codification tool for increased throughput screening. J. Biotechnol. 2011, 154:199-204. 10.1016/j.jbiotec.2011.05.012.
10. Feuk L., Carson A., Scherer S. Structural variation in the human genome. Nat. Rev. Genet. 2009, 31:771-778. 10.1038/nrg1767.
11. Hirschhorn J., Sklar P., Lindblad-Toh K., Lim Y., Ruiz-Gutierrez M., Bolk S., Langhorst B., Schaffner S., Winchester E., Lander E. SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. USA 2000, 97:12164-12169. 10.1073/pnas.210394597.
12. Kobayashi M., Rappaport E., Blasband A., Semeraro A., Sartore M., Surrey S., Fortina P. Fluorescence-based DNA minisequence analysis for detection of known single-base changes in genomic DNA. Mol. Cell. Probes 1995, 9:175-182. 10.1006/mcpr.1995.0027.
13. Mengel-Jørgensen J., Sanchez J., Børsting C., Kirpekar F., Morling N. Multiplex Y chromosome SNP genotyping using MALDI-TOF mass spectrometry. Int. Cong. Ser. 2004, 1261:15-17. 10.1016/S0531-5131(03)01544-9.
14. Mengel-Jørgensen J., Sanchez J., Børsting C., Kirpekar F., Morling N. MALDI-TOF mass spectrometric detection of multiplex single base extended primers. A study of 17 Y-chromosome single-nucleotide polymorphisms. Anal. Chem. 2004, 76:6039-6045. 10.1021/ac049264k.
15. Pastinen T., Kurg A., Metspalu A., Peltonen L., Syva A. Minisequencing: A specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 1997, 7:606-614. 10.1101/gr.7.6.606.
16. Phillips C., Fondevila M., Lareau M.V. A 34-plex autosomal SNP single base extension assay for ancestry investigations. Methods in Molecular Biology 2012, vol. 830:109-126. Humana Press, Totowa, NJ. 10.1007/978-1-61779-461-2.
17. Takatsu K., Yokomaku T., Kurata S., Kanagawa T. A FRET-based analysis of SNPs without fluorescent probes. Nucleic Acids Res. 2004, 832(19):e156. 10.1093/nar/gnh155.
18. The International HapMap Consortium A haplotype map of the human genome. Nature 2005, 437:1299-1320. 10.1038/nature04226.
19. Van Moorsel C., Van Wijngaarden E., Fokkema I., Den Dunnen J., Roos D., Van Zwieten D., Giordano P., Harteveld C. β-Globin mutation detection by tagged single-base extension and hybridization to universal glass and flow-through microarrays. Eur. J. Hum. Genet. 2004, 12:567-573. 10.1038/sj.ejhg.5201192.
20. Zienolddiny S., Skaug V. Single Nucleotide Polymorphisms as Susceptibility, Prognostic, and Therapeutic Markers of Nonsmall Cell Lung Cancer, V vol. 3 2012, 1-14. Dove Press, doi:10.2147/LCTT.S13256.