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Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

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

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 to Rui 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.

Supplementary information

Supplementary Fig. 1

SNP call rates across multiple individuals (PDF 101 kb)

Supplementary Fig. 2

Minor allele frequencies and heterozygosities (PDF 103 kb)

Supplementary Table 1

Final SNP selection (PDF 138 kb)

Supplementary Table 2

Inconsistency and inheritance errors (PDF 100 kb)

Supplementary Table 3

SNP information (PDF 107 kb)

Supplementary Table 4

Genome coverage (PDF 78 kb)

Supplementary Table 5

Individual genotypes and SNP allele frequencies (PDF 121 kb)

Supplementary Methods (PDF 136 kb)

Supplementary Manual (PDF 847 kb)

Supplementary Data 1 (ZIP 11713 kb)

Supplementary Data 2 (ZIP 4355 kb)

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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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