A self-tuning method for one-chip SNP identification

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Volumn , Issue , 2004, Pages 69-79

  Molla, Michael ^a,b   Shavlik, Jude ^a   Albert, Thomas ^b   Richmond, Todd ^b   Smith, Steven ^b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NimbleGen Systems Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BACTERIA; DATA PROCESSING; DNA; DNA SEQUENCES; GENES; NOISE ABATEMENT; PROBES; SENSITIVITY ANALYSIS; STATISTICAL METHODS; VIRUSES;

CHIP NOISE; HYBRIDIZATION EFFICIENCY; OLIGONUCLEOTIDES; SINGLE NUCLEOTIDE POLYMORPHISMS (SNP);

GENETIC ENGINEERING;

EID: 14044257867     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (12)

1. Altshuler, D.,Pollara, V., Cowles, C., Van Etten, W., Baldwin, J., Linton, L. & Lander, E., (2000). An SNP Map of the Human Genome Generated by Reduced Representation Shotgun Sequencing. Nature 407:513-516.
2. Cutler, D., Zwick, M., Carrasquillo, M., Yohn, C, Tobin, P., Kashuk, C, Mathews, D., Shah, N., Eichler, E., Warrington, J., & Chakravarti1, A. (2001). High-Throughput Variation Detection and Genotyping Using Microarrays. Genome Research 11:1913-1925.
3. Hacia, J. G. (1999). Resequencing and Mutational Analysis using Oligonucleotide Microarrays. Nature Genetics 21(1 Suppl):42-7.
4. Hirschhorn, J., Sklar, P., Lindblad-Toh, K., Lim, Y., Ruiz-Gutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Winchester, E., & Lander, E. (2000). SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. 97:12164-12169.
5. Liu, T., Moore A., & Gray, A. (2003). Efficient exact k-NN and nonparametric classification in high dimensions. Proceedings of Neural Information Processing Systems.
6. Mitchell, T. M. (1997). Machine Learning. McGraw-Hill, New York.
7. Nuwaysir, E., Huang, W., Albert, T., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T, Berg, J. P., Ballin, J., McCormick, M., Norton, J., Pollock, T., Sumwalt, T., Butcher, L., Porter, D., Molla, M., Hall, C., Blattner, F., Sussman, M., Wallace, R., Cerrina, F., & Green, R. (2002). Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography. Genome Research 12:1749-1755.
8. Ruan, Y.J., Wei, C.L., Ee, A.L., Vega, V.B., Thoreau, H., Su, S.T., Chia, J.M., Ng, P., Chiu, K.P., Lim, L., Zhang, T., Peng, C.K., Lin, E.O., Lee, N.M., Yee, S.L., Ng, L.F., Chee, R.E., Stanton, L.W., Long, P.M., & Liu. E.T., (2003). Comparative Full-Length Genome Sequence Analysis of 14 SARS Coronavirus Isolates and Common Mutations Associated with Putative Origins of Infection. Lancet 361:1779-1785.
9. Saiki, R., Walsh, P., Levenson, C. & Erlich, H. A., (1989). Genetic Analysis of Amplified DNA with Immobilized Sequence-Specific Oligonucleotide Probes. Proc. Natl. Acad. Sci. USA 86:6230-6234
10. Singh-Gasson, S., Green, R., Yue, Y., Nelson, C., Blattner, F.R., Sussman, M.R., & Cerrina, F. (1999). Maskless Fabrication of Light-Directed Oligonucleotide Microarrays using a Digital Micromirror Array. Nature Biotechnology. 17,:974-978.
11. Wang,D., Fan,J., Siao,C., Berno,A., Young,P., Sapolsky,R., Ghandour,G., Preking,N., Winchester,E., Spencer,J., Kruglyak,L., Stein,L., Hsie,L., Topaloglou,T.,Hubbell,E., Robinson,E., Mittmann,M., Morris,M., Shen,N., Kilburn,D., Rioux,J., Nusbaum,C., Rozen,S., Hudson,T., Lipshutz,R., Chee,M., & Lander,E.(1998) Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome Science280:1077-1082.
12. Wong C., Albert, T., Vega V., Norton, J., Cutler D., Richmond, T., Stanton, L., Liu, E. & Miller, L. (2004). Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays. Genome Research, accepted for publication.