Whole-genome genotyping with the single-base extension assay (original) (raw)

• Brief Communication
• Published: 20 December 2005
• Weihua Chang1,
• Grace Lee1 nAff2,
• David L Barker1,
• Richard Shen1 &
• …
• Kevin L Gunderson1

Nature Methods volume 3, pages 31–33 (2006)Cite this article

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Abstract

We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scalability, throughput and accuracy of the system by resequencing homozygous loci from our 100k Human-1 Genotyping BeadChip.

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Acknowledgements

We thank C. Allred for help with the grant applications and administration, M. Hansen for assistance in data analysis, E. Johnson, M. Graige and manufacturing department for bead pools and arrays, N. Espinosa and J. Stuelpnagel for manuscript suggestions. This work was supported in part by grants from the US National Institutes of Health (2R44CA103406-02) and National Cancer Institute (1R43CA108391-01).

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Author notes

1. Grace Lee
   Present address: Veridex LLC, Johnson & Johnson, 3210 Merryfield Row, San Diego, California, 92121, USA

Authors and Affiliations

1. Illumina, Inc., 9885 Towne Centre Drive, San Diego, 92121, California, USA
   Frank J Steemers, Weihua Chang, Grace Lee, David L Barker, Richard Shen & Kevin L Gunderson

Authors

1. Frank J Steemers
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2. Weihua Chang
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3. Grace Lee
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4. David L Barker
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5. Richard Shen
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6. Kevin L Gunderson
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Corresponding author

Correspondence toKevin L Gunderson.

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All authors have a financial interest in Illumina either via employment and/or stock ownership.

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Steemers, F., Chang, W., Lee, G. et al. Whole-genome genotyping with the single-base extension assay.Nat Methods 3, 31–33 (2006). https://doi.org/10.1038/nmeth842

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• Received: 04 October 2005
• Accepted: 10 November 2005
• Published: 20 December 2005
• Issue Date: January 2006
• DOI: https://doi.org/10.1038/nmeth842

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