Abstract
Whole genome association studies have recently been enabled by combining tag SNP information derived from the International HapMap project with novel whole genome genotyping array technologies. In particular, Infinium® whole genome genotyping (WGG) technology now has the power to genotype over 1 million SNPs on a single array. Additionally, this assay provides access to virtually any SNP in the genome enabling selection of optimized SNP content . In this chapter, we provide an overview of the tag SNP-based selection strategy for Infinium whole-genome genotyping BeadChips, including the Human 1 M BeadChip. These advances in both SNP content and technology have enabled both large-scale whole-genome disease association (WGAS) and copy number variation (CNV) studies with the ultimate goal of identifying common genetic variants, disease-associated loci, proteins, and biomarkers.
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Acknowledgments
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, oligo 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 whole genome genotyping research was funded, in part, by grants from the NIH/NCI.
Illumina, Solexa, Sentrix, Array of Arrays, BeadArray, DASL, Infinium, GoldenGate, BeadXpress, VeraCode, Oligator, IntelliHyb, iSelect, CSPro and Making Sense Out of Life are registered trademarks or trademarks of Illumina Inc. All other brands and names contained herein are the property of their respective owners.
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Peiffer, D.A., Gunderson, K.L. (2009). Design of Tag SNP Whole Genome Genotyping Arrays. In: Dufva, M. (eds) DNA Microarrays for Biomedical Research. Methods in Molecular Biology, vol 529. Humana Press. https://doi.org/10.1007/978-1-59745-538-1_4
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DOI: https://doi.org/10.1007/978-1-59745-538-1_4
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