RT Journal
A1 Hardenbol, Paul
A1 Yu, Fuli
A1 Belmont, John
A1 MacKenzie, Jennifer
A1 Bruckner, Carsten
A1 Brundage, Tiffany
A1 Boudreau, Andrew
A1 Chow, Steve
A1 Eberle, Jim
A1 Erbilgin, Ayca
A1 Falkowski, Mat
A1 Fitzgerald, Ron
A1 Ghose, Sy
A1 Iartchouk, Oleg
A1 Jain, Maneesh
A1 Karlin-Neumann, George
A1 Lu, Xiuhua
A1 Miao, Xin
A1 Moore, Bridget
A1 Moorhead, Martin
A1 Namsaraev, Eugeni
A1 Pasternak, Shiran
A1 Prakash, Eunice
A1 Tran, Karen
A1 Wang, Zhiyong
A1 Jones, Hywel B.
A1 Davis, Ronald W.
A1 Willis, Thomas D.
A1 Gibbs, Richard A.
T1 Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay
JF Genome Research 
JO Genome Research 
YR 2005 
FD February 01 
VO 15 
IS 2 
SP 269 
OP 275 
DO 10.1101/gr.3185605 
UL http://genome.cshlp.org/content/15/2/269.abstract 
AB 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.