Whole-Genome Genotyping on Bead Arrays

  • Kevin L. Gunderson
Part of the Methods in Molecular Biology book series (MIMB, volume 529)


In this review, we describe the laboratory implementation of Infinium® whole genome genotyping (WGG) technology for whole genome association studies and copy number studies. Briefly, the Infinium WGG assay employs a single tube whole genome amplification reaction to amplify the entire genome; genomic loci of interest are captured on an array by specific hybridization of picomolar concentrations amplified gDNA. After target capture, single nucleotide polymorphisms (SNPs) are genotyped on the array by a primer extension reaction using hapten-labeled nucleotides. The resultant hapten signal is amplified by immunhistochemical sandwich staining and the array is read out on a high resolution confocal scanner. We have combined this Infinium assay with high-density BeadChips to create the first array platform capable of genotyping over 1 million SNPs per slide. Additionally, the complete Infinium assay is automated using Tecan GenePaintTM slide processing system. Hybridization, washing, array-based primer extension and staining are performed directly in the Tecan capillary gap Te-Flow Through chambers. This automation process greatly increases assay robustness and throughput while enabling Laboratory Information Management System (LIMS) control of sample tracking. Finally, we give several examples of how this advance in genotyping technology is being applied in whole genome association and copy number studies.

Key words

Arrays genotyping SNP whole genome association whole genome amplification (WGA) Infinium® DNA copy number 



The technology development summarized here would not have been possible without the efforts of many dedicated individuals. We would like to thank the people at Illumina for their valuable contributions in molecular biology, automation, oligonucleotide synthesis, chemistry, engineering, bioinformatics, software, manufacturing, and process development. Special thanks go to John Stuelpnagel, Cynthia Allred, and Rose Espejo for careful reading of the manuscript. The WGG research was funded, in part, by grants from the NIH/NCI.

Illumina, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iSelect, and CSPro are registered trademarks or trademarks of Illumina. All other brands and names contained herein are the property of their respective owners.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Kevin L. Gunderson
    • 1
  1. 1.Illumina, IncSan DiegoUSA

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