Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA

Nucleic Acids Research

Volumn 34, Issue 6, 2006, Pages

  Pettersson, Erik ^a   Lindskog, Mats ^a   Lundeberg, Joakim ^a   Ahmadian, Afshin ^a  

^a ALBANOVA UNIVERSITY CENTER   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; TRINUCLEOTIDE; CYTIDINE TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE; PYRIMIDINE NUCLEOTIDE; THYMIDINE 5'-TRIPHOSPHATE; THYMIDINE TRIPHOSPHATE;

ARTICLE; CANCER; COMPUTER PROGRAM; DNA MICROARRAY; GENE AMPLIFICATION; GENE LOCUS; GENETIC VARIABILITY; GENOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; PHENOTYPE; PRIORITY JOURNAL; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; CHEMISTRY; EVALUATION; GENOME; GENOMICS; METHODOLOGY; POLYMERASE CHAIN REACTION;

CYTIDINE TRIPHOSPHATE; GENOME, HUMAN; GENOMICS; GENOTYPE; GUANOSINE TRIPHOSPHATE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; THYMINE NUCLEOTIDES;

EID: 33645832164     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl103     Document Type: Article

References (20)

1. Wang,D.G., Fan,J.B., Siao,C.J., Berno,A., Young,P., Sapolsky,R., Ghandour,G., Perkins,N., Winchester,E., Spencer,J. et al. (1998) Large-scale identification, mapping, and genotyping of single- nucleotide polymorphisms in the human genome. Science, 280, 1077-1082.
2. Hirschhorn,J.N., Sklar,P., Lindblad-Toh,K., Lim,Y.M., Ruiz-Gutierrez,M., Bolk,S., Langhorst,B., Schaffner,S., Winchester,E. and Lander,E.S. (2000) SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl Acad. Sci. USA, 97, 12164-12169.
3. Nilsson,M., Malmgren,H., Samiotaki,M., Kwiatkowski,M., Chowdhary,B.P. and Landegren,U. (1994) Padlock probes: Circularizing oligonucleotides for localized DNA detection. Science, 265, 2085-2088.
4. O'Meara,D., Ahmadian,A., Odeberg,J. and Lundeberg,J. (2002) SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays. Nucleic Acids Res., 30, e75.
5. Nilsson,M., Baner,J., Mendel-Hartvig,M., Dahl,F., Antson,D.O., Gullberg,M. and Landegren,U. (2002) Making ends meet in genetic analysis using padlock probes. Hum. Mutat., 19, 410-415.
6. Landegren,U. and Nilsson,M. (1997) Locked on target: Strategies for future gene diagnostics. Ann. Med., 29, 585-590.
7. Hultin,E., Kaller,M., Ahmadian,A. and Lundeberg,J. (2005) Competitive enzymatic reaction to control allele-specific extensions. Nucleic Acids Res., 33, e48.
8. Holmberg,A., Blomstergren,A., Nord,O., Lukacs,M., Lundeberg,J. and Uhlen,M. (2005) The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis, 26, 501-510.
9. Kennedy,G.C., Matsuzaki,H., Dong,S., Liu,W.M., Huang,J., Liu,G., Su,X., Cao,M., Chen,W., Zhang,J. et al. (2003) Large-scale genotyping of complex DNA. Nature Biotechnol., 21, 1233-1237.
10. Dahl,F., Gullberg,M., Stenberg,J., Landegren,U. and Nilsson,M. (2005) Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res., 33, e71.
11. Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A., Berka,J., Braverman,M.S., Chen,Y.J., Chen,Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
12. Gunderson,K.L., Steemers,F.J., Lee,G., Mendoza,L.G. and Chee,M.S. (2005) A genome-wide scalable SNP genotyping assay using microarray technology. Nature Genet., 37, 549-554.
13. Wang,H.Y., Luo,M., Tereshchenko,I.V., Frikker,D.M., Cui,X., Li,J.Y., Hu,G., Chu,Y., Azaro,M.A., Lin,Y. et al. (2005) A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome. Genome Res., 15, 276-283.
14. Fan,J.B., Oliphant,A., Shen,R., Kermani,B.G., Garcia,F., Gunderson,K.L., Hansen,M., Steemers,F., Butler,S.L., Deloukas,P. et al. (2003) Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol., 68, 69-78.
15. Hardenbol,P., Baner,J., Jain,M., Nilsson,M., Namsaraev,E.A., Karlin-Neumann,G.A., Fakhrai-Rad,H., Ronaghi,M., Willis,T.D., Landegren,U. et al. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol., 21, 673-678.
16. Newton,C.R., Graham,A., Heptinstall,L.E., Powell,S.J., Summers,C., Kalsheker,N., Smith,J.C. and Markham,A.F. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res., 17, 2503-2516.
17. Bergen,A.W., Qi,Y., Haque,K.A., Welch,R.A. and Chanock,S.J. (2005) Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance. BMC Biotechnol., 5, 24.
18. Bergen,A.W., Haque,K.A., Qi,Y., Beerman,M.B., Garcia-Closas,M., Rothman,N. and Chanock,S.J. (2005) Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources. Hum. Mutat., 26, 262-270.
19. Maschke,K.J. (2005) Navigating an ethical patchwork-human gene banks. Nat. Biotechnol., 23, 539-545.
20. Steemers,F.J., Chang,W., Lee,G., Barker,D.L., Shen,R. and Gunderson,K.L. (2006) Whole-genome genotyping with the single-base extension assay. Nature Meth., 3, 31-33.