Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays (original) (raw)

• Brief Communication
• Published: 21 October 2004
• Shoulian Dong1,
• Halina Loi1,
• Xiaojun Di1,
• Guoying Liu1,
• Earl Hubbell1,
• Jane Law1,
• Tam Berntsen1,
• Monica Chadha1,
• Henry Hui1,
• Geoffrey Yang1,
• Giulia C Kennedy1,
• Teresa A Webster1,
• Simon Cawley1,
• P Sean Walsh1,
• Keith W Jones1,
• Stephen P A Fodor1 &
• …
• Rui Mei1

Nature Methods volume 1, pages 109–111 (2004)Cite this article

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Abstract

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.

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Figure 1: Performance at various call rates.

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Acknowledgements

We are grateful to G. Marcus, R. Chiles, M. Shapero, J. Huang, F. Christians, C. Rosenow, D. Kulp, D. Bartell, S. Narasimhan, M. Shen, M. Mittmann, J. McAuliffe, S. Mitra, J. Chen, M. Cao and A. He for valuable discussions and for providing data.

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Authors and Affiliations

1. Affymetrix, Inc., 3380 Central Expressway, Santa Clara, 95051, California, USA
   Hajime Matsuzaki, Shoulian Dong, Halina Loi, Xiaojun Di, Guoying Liu, Earl Hubbell, Jane Law, Tam Berntsen, Monica Chadha, Henry Hui, Geoffrey Yang, Giulia C Kennedy, Teresa A Webster, Simon Cawley, P Sean Walsh, Keith W Jones, Stephen P A Fodor & Rui Mei

Authors

1. Hajime Matsuzaki
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2. Shoulian Dong
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3. Halina Loi
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4. Xiaojun Di
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5. Guoying Liu
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6. Earl Hubbell
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7. Jane Law
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8. Tam Berntsen
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9. Monica Chadha
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10. Henry Hui
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11. Geoffrey Yang
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12. Giulia C Kennedy
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13. Teresa A Webster
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14. Simon Cawley
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15. P Sean Walsh
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16. Keith W Jones
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17. Stephen P A Fodor
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18. Rui Mei
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Corresponding author

Correspondence toRui Mei.

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Competing interests

All of the authors are employed by Affymetrix, a commercial entity that manufactures and markets high-density oligonucleotide arrays based on the technology described in this paper.

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Matsuzaki, H., Dong, S., Loi, H. et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.Nat Methods 1, 109–111 (2004). https://doi.org/10.1038/nmeth718

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• Received: 10 August 2004
• Accepted: 22 September 2004
• Published: 21 October 2004
• Issue Date: November 2004
• DOI: https://doi.org/10.1038/nmeth718

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