[3] Illumina Universal Bead Arrays

Methods in Enzymology

Volumn 410, Issue , 2006, Pages 57-73

  Fan, Jian Bing ^a   Gunderson, Kevin L ^a   Bibikova, Marina ^a   Yeakley, Joanne M ^a   Chen, Jing ^a   Wickham Garcia, Eliza ^a   Lebruska, Lori L ^a   Laurent, Marc ^a   Shen, Richard ^a   Barker, David ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MICROSPHERE;

BIOTINYLATION; COMPUTER MODEL; COMPUTER PROGRAM; DNA METHYLATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENOTYPE; HIGH THROUGHPUT SCREENING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; HUMAN; INSTRUMENTATION; METHODOLOGY;

ANIMALS; HUMANS; MICROSPHERES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747822630     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(06)10003-8     Document Type: Review

References (35)

1. Barker D.L., Hansen M.S., Faruqi A.F., Giannola D., Irsula O.R., Lasken R.S., Latterich M., Makarov V., Oliphant A., Pinter J.H., Shen R., Sleptsova I., Ziehler W., and Lai E. Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res. 14 (2004) 901-907
2. Barker D.L., Theriault D., Che D., Dickinson T., Shen R., and Kain R. Self-assembled random arrays: High-performance imaging and genomics applications on a high-density microarray platform. Proc. SPIE 4966 (2003) 1-11
3. Bibikova M., Talantov D., Chudin E., Yeakley J.M., Chen J., Doucet D., Wickham E., Atkins D., Barker D., Chee M., Wang Y., and Fan J.B. Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am. J. Pathol. 165 (2004) 1799-1807
4. Bibikova M., Yeakley J.M., Chudin E., Chen J., Wickham E., Wang-Rodriguez J., and Fan J.B. Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysis. Clin. Chem. 50 (2004) 2384-2386
5. Botstein D., and Risch N. Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33 Suppl. (2003) 228-237
6. Braeckmans K., De Smedt S.C., Leblans M., Pauwels R., and Demeester J. Encoding microcarriers: Present and future technologies. Nat. Rev. Drug Discov. 1 (2002) 447-456
7. Chan W.C., Maxwell D.J., Gao X., Bailey R.E., Han M., and Nie S. Luminescent quantum dots for multiplexed biological detection and imaging. Curr. Opin. Biotechnol. 13 (2002) 40-46
8. Chen J., Iannone M.A., Li M.S., Taylor J.D., Rivers P., Nelsen A.J., Slentz-Kesler K.A., Roses A., and Weiner M.P. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10 (2000) 549-557
9. Fan J.B., Chen X., Halushka M.K., Berno A., Huang X., Ryder T., Lipshutz R.J., Lockhart D.J., and Chakravarti A. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10 (2000) 853-860
10. Fan J.B., Oliphant A., Shen R., Kermani B.G., Garcia F., Gunderson K.L., Hansen M., Steemers F., Butler S.L., Deloukas P., Galver L., Hunt S., McBride C., Bibikova M., Rubano T., Chen J., Wickham E., Doucet D., Chang W., Campbell D., Zhang B., Kruglyak S., Bentley D., Haas J., Rigault P., Zhou L., Stuelpnagel J., and Chee M.S. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68 (2003) 69-78
11. Fan J.B., Yeakley J.M., Bibikova M., Chudin E., Wickham E., Chen J., Doucet D., Rigault P., Zhang B., Shen R., McBride C., Li H.R., Fu X.D., Oliphant A., Barker D.L., and Chee M.S. A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 14 (2004) 878-885
12. Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., and Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 251 (1991) 767-773
13. Fulton R.J., McDade R.L., Smith P.L., Kienker L.J., and Kettman Jr. J.R. Advanced multiplexed analysis with the FlowMetrix system. Clin. Chem. 43 (1997) 1749-1756
14. Gerry N.P., Witowski N.E., Day J., Hammer R.P., Barany G., and Barany F. Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol. 292 (1999) 251-262
15. Gunderson K.L., Kruglyak S., Graige M.S., Garcia F., Kermani B.G., Zhao C., Che D., Dickinson T., Wickham E., Bierle J., Doucet D., Milewski M., Yang R., Siegmund C., Haas J., Zhou L., Oliphant A., Fan J.B., Barnard S., and Chee M.S. Decoding randomly ordered DNA arrays. Genome Res. 14 (2004) 870-877
16. Gunderson K.L., Steemers F.J., Lee G., Mendoza L.G., and Chee M.S. A genome-wide scalable SNP genotyping assay using microarray technology. Nat. Genet. 37 (2005) 549-554
17. Han M., Gao X., Su J.Z., and Nie S. Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nat. Biotechnol. 19 (2001) 631-635
18. Hinds D.A., Stuve L.L., Nilsen G.B., Halperin E., Eskin E., Ballinger D.G., Frazer K.A., and Cox D.R. Whole-genome patterns of common DNA variation in three human populations. Science 307 (2005) 1072-1079
19. Holloway A.J., van Laar R.K., Tothill R.W., and Bowtell D.D. Options available-from start to finish-for obtaining data from DNA microarrays II. Nat. Genet. 32 Suppl. (2002) 481-489
20. Iannone M.A., Taylor J.D., Chen J., Li M.S., Rivers P., SlentzKesler K.A., and Weiner M.P. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39 (2000) 131-140
21. Knight J.C. Allele-specific gene expression uncovered. Trends Genet. 20 (2004) 113-116
22. Kuhn K., Baker S.C., Chudin E., Lieu M.H., Oeser S., Bennett H., Rigault P., Barker D., McDaniel T.K., and Chee M.S. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 14 (2004) 2347-2356
23. Kwok P.Y., and Chen X. Detection of single nucleotide polymorphisms. Curr. Issues Mol. Biol. 5 (2003) 43-60
24. Lockhart D.J., and Trulson M.O. Multiplex metallica. Nat. Biotechnol. 19 (2001) 1122-1123
25. Michael K.L., Taylor L.C., Schultz S.L., and Walt D.R. Randomly ordered addressable high-density optical sensor arrays. Anal. Chem. 70 (1998) 1242-1248
26. Nicewarner-Pena S.R., Freeman R.G., Reiss B.D., He L., Pena D.J., Walton I.D., Cromer R., Keating C.D., and Natan M.J. Submicrometer metallic barcodes. Science 294 (2001) 137-141
27. Oliphant A., Barker D.L., Stuelpnagel J.R., and Chee M.S. BeadArray technology: Enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques Suppl. (2002) 56-58 60-61
28. Pastinen T., and Hudson T.J. Cis-acting regulatory variation in the human genome. Science 306 (2004) 647-650
29. Pastinen T., Sladek R., Gurd S., Sammak A., Ge B., Lepage P., Lavergne K., Villeneuve A., Gaudin T., Brandstrom H., Beck A., Verner A., Kingsley J., Harmsen E., Labuda D., Morgan K., Vohl M.C., Naumova A.K., Sinnett D., and Hudson T.J. A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genom. 16 (2004) 184-193
30. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
31. Shen R., Fan J.B., Campbell D., Chang W., Chen J., Doucet D., Yeakley J., Bibikova M., Wickham Garcia E., McBride C., Steemers F., Garcia F., Kermani B.G., Gunderson K., and Oliphant A. High-throughput SNP genotyping on universal bead arrays. Mutat. Res. 573 (2005) 70-82
32. Syvanen A.C. Toward genome-wide SNP genotyping. Nat. Genet. 37 Suppl. (2005) 5-10
33. The International HapMap Consortium. The International HapMap Project. Nature 426 (2003) 789-796
34. Yan H., Yuan W., Velculescu V.E., Vogelstein B., and Kinzler K.W. Allelic variation in human gene expression. Science 297 (2002) 1143
35. Yeakley J.M., Fan J.B., Doucet D., Luo L., Wickham E., Ye Z., Chee M.S., and Fu X.D. Profiling alternative splicing on fiber-optic arrays. Nat. Biotechnol. 20 (2002) 353-358