SNP Chart: An integrated platform for visualization and interpretation of microarray genotyping data

Bioinformatics

Volumn 21, Issue 1, 2005, Pages 124-127

  Tebbutt, Scott J ^a   Opushnyev, Igor V ^a   Tripp, Ben W ^a   Kassamali, Ayaz M ^a   Alexander, Wendy L ^a   Andersen, Marilyn I ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMISTRY; COMPUTER LANGUAGE; COMPUTER SYSTEM; DNA MICROARRAY; GENE PROBE; GENE REPLICATION; GENETIC ANALYSIS; GENOTYPE; PRIORITY JOURNAL; QUALITY CONTROL; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 12744269458     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth470     Document Type: Article

References (16)

1. 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.
2. Buetow,K.H., Edmonson,M., MacDonald,R., Clifford,R., Yip,P., Kelley,J., Little,D.P., Strausberg,R., Koester,H., Cantor,C.R. and Braun,A. (2001) High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl Acad. Sci. USA, 98 581-584.
3. Chan,K., Wong,M.S., Chan,T.K. and Chan,V. (2004) A thalassaemia array for Southeast Asia. Br. J. Haematol., 124, 232-239.
4. Dawson,E., Abecasis,G.R., Bumpstead,S., Chen,Y., Hunt,S., Beare,D.M., Pabial,J., Dibling,T., Tinsley,E., Kirby,S. et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418, 544-548.
5. Gemignani,F., Perra,C., Landi,S., Canzian,F., Kurg,A., Tonisson,N., Galanello,R., Cao,A., Metspalu,A. and Romeo,G. (2002) Reliable detection of beta-thalassemia and G6PD mutations by a DNA microarray. Clin. Chem., 48, 2051-2054.
6. 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.
7. 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. Nat. Biotechnol., 21, 1233-1237.
8. Kurg,A., Tonisson,N., Georgiou,I., Shumaker,J., Tollett,J. and Metspalu,A. (2000) Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet. Test, 4, 1-7.
9. Landi,S., Gemignani,F., Gioia-Patricola,L., Chabrier,A. and Canzian,F. (2003) Evaluation of a microarray for genotyping polymorphisms related to xenobiotic metabolism and DNA repair. BioTechniques, 35, 816-820, 822, 824-817.
10. Livak,K.J., Flood,S.J., Marmaro,J., Giusti,W. and Deetz,K. (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl., 4, 357-362.
11. Oliphant,A., Barker,D.L., Stuelpnagel,J.R. and Chee,M.S. (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. BioTechniques, (Suppl. 56-58, 60-51.
12. Risch,N. and Merikangas,K. (1996) The future of genetic studies of complex human diseases. Science, 273, 1516-1517.
13. Sanger,F., Nicklen,S. and Coulson,A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74 5463-5467.
14. Shumaker,J.M., Metspalu,A. and Caskey,C.T. (1996) Mutation detection by solid phase primer extension. Hum. Mutat., 7, 346-354.
15. Tebbutt,S.J., Burkett,K.M., He,J-Q., Ruan,J., Opushnyev,I.V., Tripp,B.W., Zeznik,J.A., Abara,C.O., Nelson,C.C. and Walley,K.R. (2004) A microarray genotyping resource to determine population stratification in genetic association studies of complex disease. Bio Techniques, in press.
16. 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, 1077-1081