Minisequencing on functionalised self-assembled monolayer as a simple approach for single nucleotide polymorphism analysis of cattle

Zeitschrift fur Naturforschung - Section C Journal of Biosciences

Volumn 58, Issue 5-6, 2003, Pages 413-420

  Du, Weidong ^a   Cieplik, Michael ^b   Durstewitz, Gregor ^c   Sarkar, Chandra Mohan ^b   Kruschina, Margit ^b   Fries, Rudi ^c   Ortigao, Flavio Ramalho ^a  

^a Antarus LifeScience GmbH   (Germany)

^b Thermo Hybaid GmbH   (Germany)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Microarray; Minisequencing; SNP

Indexed keywords

ANIMALIA; BOS TAURUS; MAMMALIA;

EID: 0038646609     PISSN: 09395075     EISSN: None     Source Type: Journal    
DOI: 10.1515/znc-2003-5-621     Document Type: Article

References (41)

1. Altschul S. F., Gish W., Miller W., Myers E. W., and Lipman D. J. (1990), Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Ahmadian A., Gharizadeh B., Gustafsson A. C., Sterky F., Nyren P., Uhlen M., and Lundeberg J. (2000), Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280, 103-110.
3. Ahrendt S. A., Halachmi S., Chow J. T., Wu L., Halachmi N., Yang S. C., Wehage S., Jen J., and Sidransky D. (1999), Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array. Proc. Natl. Acad. Sci. USA 96, 7382-7387.
4. Bain C. D., Evall J., and Whitesides G. M. (1989), Formation of monolayers by coadsorption of thiols on gold: Variation in the head group, tail group, and solvent. J. Am. Chem. Soc. 111, 7155-7164.
5. Barendse W., and Armitage S. M. (2001), The single strand conformational analysis of cattle and human single nucleotide polymorphisms may be biased towards specific sequence motifs that minimize local secondary structure of single strand DNA. Anim. Biotechnol. 12, 21-28.
6. Baron H., Fung S., Aydin A., Bahring S., Luft F. C., and Schuster H. (1996), Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nat. Biotechnol. 14, 1279-1282.
7. Brookes A. J., Lehvaslaiho H., Siegfried M., Boehm J. G., Yuan Y. P., Sarkar C. M., Bork P., and Ortigao F. (2000), HGBASE: a database of SNPs and other variations in and around human genes. Nucleic Acids Res. 28, 356-360.
8. Buitkamp J., Antes R., and Wagner V. (1999), DNA profiling in veterinary medicine. In: DNA Profiling and DNA Fingerprinting (J. T. Epplen, and T. Lubjuhn, eds.). Birkhäuser, Basel, p. 53-70.
9. Conner B. J., Reyes A. A., Morin C., Itakura K., Teplitz R. L., and Wallace R. B. (1983), Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 80, 278-282.
10. Durstewitz G., Buitkamp J., Kollers S., and Fries R. (2000), www.SNPZoo.de. Poster presentation at the 27th International Conference on Animal Genetics. Minneapolis, USA, July.
11. Etzold T., Ulyanov A., and Argos P. (1996), SRS: information retrieval system for molecular biology data banks. Methods Enzymol. 266, 114-128.
12. Fears S., Chakrabanti S. R., Nucifora G., and Rowley J. D. (2002), Differential expression of TCL1 during pre-B-cell acute lymphoblastic leukemia progression. Cancer Genet. Cytogenet. 135, 110-119.
13. Fries R., Ewald D., Thaller G., and Buitkamp J. (2001), Assessment of the nucleotide sequence variability in the bovine T-cell receptor alpha delta joining gene region. Anim. Biotechnol. 12, 29-49.
14. Fries R., and Durstewitz G. (2001), Digital DNA signatures for animal tagging. Nat. Biotechnol. 19, 508.
15. Hacia J. G., Brody L. C., Chee M. S., Fodor S. P., and Collins F. S. (1996), Detection of heterozygous mutations in BRCA1 using high-density oligonucleotide array and two-colour fluorescence analysis. Nat. Genet. 14, 441-447.
16. Hacia J. G., Sun B., Hunt N., Edgemon K., Mosbrook D., Robbins C., Fodor S. P., Tagle D. A., and Collins F. S. (1998), Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays. Genome Res. 8, 1245-1258.
17. Heaton M. P., Grosse W. M., Kappes S. M., Keele J. W., Chitko-McKown C. G., Cundiff L. V., Braun A., Little D. P., and Laegreid W. W. (2001a), Estimation of DNA sequence diversity in bovine cytokine genes. Mamm. Genome 12, 32-37.
18. Heaton M. P., Chitko-McKnown C. G., Grosse W. M., Keele J. W., Keen J. E., and Laegreid W. W. (2001b), Interleukin-8 haplotype structure from nucleotide sequence variation in commercial population of U. S. beef cattle. Mamm. Genome 12, 219-226.
19. Heaton M. P., Harhay G. P., Bennett G. L., Stone R. T., Grosse W. M., Casas E., Keele J. W., Smith T. P., Chitko-McKown C. G., and Laegreid W. W. (2002), Selection and use of SNP markers for animal identification and paternity analysis in U. S. beef cattle. Mamm. Genome 13, 272-281
20. Huang J. X., Mehrens D., Wiese R., Lee S., Tam S. W., Daniel S., Gilmore J., Shi M., and Lashkari D. (2001), High-throughput genomic and proteomic analysis using microarray technology. Clin. Chem. 47, 1912-1916.
21. Jazaeri A. A., Yee C. J., Sotiriou C., Brantley K. R., Boyd J., and Liu E. T. (2002), Gene expression profilings of BRCA1-linked, BRCA2-linked and sporadic ovarian cancers. J. Natl. Cancer Inst. 94, 990-1000.
22. Karan D., Kelly D. L., Rizzino A,. Lin M. F., and Batra S. K. (2002), Expression profiling of differentially-regulated genes during progression of androgen-independent growth in human prostate cancer cells. Carcinogenesis 23, 967-976.
23. Konfortov B. A., Licence V. E., and Miller J. R. (1999), Re-sequencing of DNA from a diverse panel of cattle reveals a high level of polymorphism in both intron and exon. Mamm. Genome 10, 1142-1145.
24. Kwok P. Y. (2001), Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2,235-258.
25. Lien S., Rogne S. Brovold M. J., and Aleström P. (1990), A method for isolation of DNA from frozen (A. I.) bull semen. J. Anim. Breed Genet. 107, 74.
26. Livak K. J., and Hainer J. W. (1994), A microtiter plate assay for determining apolipoprotein E genotype and discovery of a rare allele. Hum. Mutat. 3, 379-385.
27. Lopez-Crapez E., Livache T., Marchand J., and Grenier J. (2001), K-ras mutation detection by hybridization to a polypyrrole DNA chip. Clin. Chem. 47, 186-194.
28. Maskos U., and Southern E. M. (1993), A novel method for the parallel analysis of multiple mutations in multiple samples. Nucleic Acids Res. 21, 2269-2270.
29. Mecklenburg M., Danielsson B., and Winqvist F. (1996), Broad Specific Arrays: A qualitative Approach to Complex Sample Discrimination. Patent SE, PCT/EP 97/03317.
30. Mrksich M., and Whitesides G. M. (1996), Using self-assembled monolayers to understand the interactions of man-made surfaces with proteins and cells. Annu. Rev. Biophys. Biomol. Struct. 25, 55-78.
31. Nikiforov T. T., Rendle R. B., Goelet P., Rogers Y. H., Kotewicz M. L., Anderson S., Trainor G. L., and Knapp M. R. (1994), Genetic bit analysis: a solid phase method for typing signal nucleotide polymorphisms. Nucleic Acids Res. 22, 4167-4175.
32. Nurmi J., Kiviniemi M., Kujanpaa M., Sjoroos M., Ilonen J., and Lovgren T. (2001), High-throughput genetic analysis using time-resolved fluoremetry and closed-tube detection. Anal. Biochem. 299, 211-217.
33. Pastinen T., Kurg A., Metspalu A., Peltonen L., and Syvänen A. C. (1997), Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7, 606-614.
34. Persson H. H. J., Caseri W. R., and Suter U. W. (2001), Versatile method for chemical reactions with self-assembled monolayers of alkanethiol on gold. Langmuir 17, 3643-3650
35. Raitio M., Lindroos K., Laukkanen M., Pastinen T., Sistonen P., Sajantila A., and Syvänen A. C. (2001), Y-chromosomal SNPs in Finno-Ugric-speaking populations analyzed by minisequencing on microarrays. Genome Res. 11, 471-482.
36. Sauer S., Lechner D., Berlin K., Plancon C., and Heuermann A. (2000), Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res. 28, E100.
37. Shi M. M. (2001), Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotying technologies. Clin. Chem. 47, 164-172
38. Syvänen A. C. (1994), Detection of point mutations in human genes by the solid-phase minisequencing method. Clin. Chim. Acta 226, 225-236.
39. Ulman A. (1996), Formation and structure of self-assembled monolayers. Chem. Rev. 96, 1533-1554
40. Wang Z., Liu Y., Mori M., and Mulesz-Martin M. (2002), Gene expression profiling of initiated epidermal cells with benign or malignant tumor fates. Carcinogenesis 23, 635-643.
41. Warrington J. A., Shah N. A., Chen X., Janis M., Liu C., Kondapalli S., Reyes V., Savage M. P., Zhang Z., Watts R., DeGuzman M., Berno A., Snyder J., and Baid J. (2002), New developments in high-throughput resequencing and variation detection using high density microarrays. Hum. Mutat. 19, 402-409.