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Genome Res. 15:269-275, 2005
©2005 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/05 $5.00
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Methods

Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay

Paul Hardenbol1, Fuli Yu2, John Belmont2, Jennifer MacKenzie1, Carsten Bruckner1, Tiffany Brundage1, Andrew Boudreau1, Steve Chow1, Jim Eberle1, Ayca Erbilgin1, Mat Falkowski1, Ron Fitzgerald1, Sy Ghose2, Oleg Iartchouk1, Maneesh Jain1, George Karlin-Neumann1, Xiuhua Lu2, Xin Miao1, Bridget Moore1, Martin Moorhead1, Eugeni Namsaraev1, Shiran Pasternak2, Eunice Prakash1, Karen Tran1, Zhiyong Wang1, Hywel B. Jones1, Ronald W. Davis3, Thomas D. Willis1,4 and Richard A. Gibbs2

1 ParAllele BioScience, Inc., South San Francisco, California 94080, USA 2 Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas 77030, USA 3 Stanford Genome Technology Center, Stanford University, California 94305, USA

Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP assays using this technology in a population of 30 trios from the Centre d'Etude Polymorphisme Humain family panel as part of the International HapMap project, we established SNP conversion rates of ~90% with concordance rates >99.6% and completeness levels >98% for assays multiplexed up to 12,000plex levels. Furthermore, these individual metrics can be "traded off" and, by sacrificing a small fraction of the conversion rate, the accuracy can be increased to very high levels. No loss of performance is seen when scaling from 6,000plex to 12,000plex assays, strongly validating the ability of the technology to suppress cross-reactivity at high multiplex levels. The results of this study demonstrate the suitability of this technology for comprehensive association studies that use targeted SNPs in indirect linkage disequilibrium studies or that directly screen for causative mutations.

4 Corresponding author.
E-mail tom{at}p-gene.com; fax (650) 228-7405.

Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.3185605.


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