Highly parallel SNP genotyping

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 68, Issue , 2003, Pages 69-78

  Fan, J B ^a   Oliphant, A ^a   Shen, R ^a   Kermani, B G ^a   Garcia, F ^a   Gunderson, K L ^a   Hansen, M ^a   Steemers, F ^a   Butler, S L ^a,c   Deloukas, P ^b   Galver, L ^a   Hunt, S ^b   McBride, C ^a   Bibikova, M ^a   Rubano, T ^a   Chen, J ^a   Wickham, E ^a   Doucet, D ^a   Chang, W ^a   Campbell, D ^a   Zhang, B ^a,d   Kruglyak, S ^a   Bentley, D ^b   Haas, J ^a,e   Rigault, P ^a   Zhou, L ^a   Stuelpnagel, J ^a   Chee, M S ^a   more..

^a Llumina Inc   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United States)

^d ACTIVX BIOSCIENCES INC   (United States)

^e NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOANALYSIS; CLINICAL GENETICS; CONFERENCE PAPER; DNA DETERMINATION; DNA SCREENING; GENE IDENTIFICATION; GENE TECHNOLOGY; GENETIC PROCEDURES; GENOME ANALYSIS; GENOTYPE; HUMAN; PRIORITY JOURNAL; RNA ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ARTICLE; AUTOMATION; BEAD ARRAY READER; CHROMOSOME ANALYSIS; DIAGNOSTIC ACCURACY; DNA SYNTHESIS; GENE CONTROL; GENE CONVERSION; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; HUMAN CHROMOSOME; ILLUMINATION; IMAGING SYSTEM; IMMUNOASSAY; LABORATORY DEVICE; MEDICAL INFORMATION SYSTEM; MULTIPLEX POLYMERASE CHAIN REACTION; QUALITY CONTROL; REPRODUCIBILITY;

DNA; DNA POLYMERASE; MESSENGER RNA; OLIGONUCLEOTIDE; RNA;

EID: 2442667212     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2003.68.69     Document Type: Conference Paper

References (28)

1. Abravaya K., Carrino J.J., Muldoon S., and Lee H.H. 1995. Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res. 23: 675.
2. Barker D.L., Therault G., Che D., Dickinson T., Shen R., and Kain R. 2003. Self-assembled random arrays: High-performance imaging and genomics applications on a high-density microarray platform. Proc. SPIE 4966: 1.
3. Cai H., White P.S., Torney D., Deshpande A., Wang Z., Keller R.A., Marrone B., and Nolan J.P. 2000. Flow cytometry-based minisequencing: A new platform for high-throughput single-nucleotide polymorphism scoring. Genomics 66: 135.
4. 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. 2000. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10: 549.
5. Dawson E., Abecasis G.R., Bumpstead S., Chen Y., Hunt S., Beare D.M., Pabial J., Dibling T., Tinsley E., Kirby S., Carter D., Papaspyridonos M., Livingstone S., Ganske R., Lohmussaar E., Zernant J., Tonisson N., Remm M., Magi R., Puurand T., Vilo J., Kurg A., Rice K., Deloukas P., and Mott R., et al. 2002. A first-generation linkage disequilibrium map of human chromosome 22. Nature 418: 544.
6. Fan J.B., Chen X., Halushka M.K., Berno A., Huang X., Ryder T., Lipshutz R.J., Lockhart D.J., and Chakravarti A. 2000. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10: 853.
7. Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J., Blumenstiel B., Higgins J., DeFelice M., Lochner A., Faggart M., Liu-Cordero S.N., Rotimi C., Adeyemo A., Cooper R., Ward R., Lander E.S., Daly M.J., and Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225.
8. Gerry N.P., Witowski N.E., Day J., Hammer R.P., Barany G., and Barany F. 1999. Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol. 292: 251.
9. Gunderson K.L., Kruglyak S., Graige M.S., Garcia F., Kermani B., 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. 2004. Decoding randomly ordered DNA arrays. Genome Res. (in press).
10. 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., and Davis R. W. 2003. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21: 673.
11. Iannone M.A., Taylor J.D., Chen J., Li M.S., Rivers P., Slentz-Kesler K.A., and Weiner M.P. 2000. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39: 131.
12. Kennedy G.C., Matsuzaki H., Dong S., Liu W.M., Huang J., Liu G., Su X., Cao M., Chen W., Zhang J., Liu W., Yang G., Di X., Ryder T., He Z., Surti U., Phillips M.S., Boyce-Jacino M.T., Fodor S.P., and Jones K.W. 2003. Large-scale genotyping of complex DNA. Nat. Biotechnol. 21: 1233.
13. Kwok P.Y. 2001. Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2: 235.
14. Lebl M., Burger C., Ellman B., Fambro S., Hachmann J., Heiner D., Ibrahim G., Jones A., Kim S., Nibbe M., Pires J., Santos C., Touhy S., Mudra P., Pokorny V., Poncar P., and Zenisek K. 2001. Fully automated parallel oligonucleotide synthesizer. Collect. Czech. Chem. Commun. 66: 1299.
15. Lo H.S., Wang Z., Hu Y., Yang H.H., Gere S., Buetow K.H., and Lee M. P. 2003. Allelic variation in gene expression is common in the human genome. Genome Res. 13: 1855.
16. Michael K.L., Taylor L.C., Schultz S.L., and Walt D.R. 1998. Randomly ordered addressable high-density optical sensor arrays. Anal. Chem. 70: 1242.
17. Ohnishi Y., Tanaka T., Ozaki K., Yamada R., Suzuki H., and Nakamura Y. 2001. A high-throughput SNP typing system for genome-wide association studies. J. Hum. Genet. 46: 471.
18. 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 32: S56.
19. Pastinen T., Raitio M., Lindroos K., Tainola P., Peltonen L., and Syvanen A.C. 2000. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10: 1031.
20. Patil N., Berno A.J., Hinds D.A., Barrett W.A., Doshi J.M., Hacker C.R., Kautzer C.R., Lee D.H., Marjoribanks C., McDonough D.P., Nguyen B.T., Norris M.C., Sheehan J.B., Shen N., Stern D., Stokowski R.P., Thomas D.J., Trulson M.O., Vyas K.R., Frazer K.A., Fodor S.P., and Cox D.R. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719.
21. Phillips M.S., Lawrence R., Sachidanandam R., Morris A.P., Balding D.J., Donaldson M.A., Studebaker J.F., Ankener W.M., Alfisi S.V., Kuo F.S., Camisa A.L., Pazorov V., Scott K.E., Carey B.J., Faith J., Katari G., Bhatti H.A., Cyr J.M., Derohannessian V., Elosua C., Forman A.M., Grecco N.M., Hock C.R., Kuebler J.M., and Lathrop J.A., et al. 2003. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33: 382.
22. Reich D.E., Gabriel S.B. and Altshuler D. 2003. Quality and completeness of SNP databases. Nat. Genet. 33: 457.
23. Sachidanandam R., Weissman D., Schmidt S.C., Kakol J.M., Stein L.D., Marth G., Sherry S., Mullikin J.C., Mortimore B.J., Willey D.L., Hunt S.E., Cole C.G., Coggill P.C., Rice C.M., Ning Z., Rogers J., Bentley D.R., Kwok P.Y., Mardis E.R., Yeh R.T., Schultz B., Cook L., Davenport R., Dante M., and Fulton L., et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928.
24. Schouten J.P., McElgunn C.J., Waaijer R., Zwijnenburg D., Diepvens F., and Pals G. 2002. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30: e57.
25. Syvanen A.C. 2001. Accessing genetic variation: Genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2: 930.
26. Wang D.G., Fan J.-B., Siao C.-J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J., Kruglyak L., Stein L., Hsie L., Topaloglou T., Hubbell E., Robinson E., Mittmann M., Morris M.S., Shen N., Kilburn D., Rioux J., Nusbaum C., Rozen S., Hudson T.J., and Lipshutz R., et al. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280: 1077.
27. Yan H., Yuan W., Velculescu V.E., Vogelstein B., and Kinzler K. W. 2002. Allelic variation in human gene expression. Science 297: 1143.
28. Yeakley J.M., Fan J.B., Doucet D., Luo L., Wickham E., Ye Z., Chee M.S., and Fu X.D. 2002. Profiling alternative splicing on fiber-optic arrays. Nat. Biotechnol. 20: 353.