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

TitleHighly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.
Publication TypeJournal Article
Year of Publication2005
AuthorsHardenbol, P, Yu, F, Belmont, J, Mackenzie, J, Bruckner, C, Brundage, T, Boudreau, A, Chow, S, Eberle, J, Erbilgin, A, Falkowski, M, Fitzgerald, R, Ghose, S, Iartchouk, O, Jain, M, Karlin-Neumann, G, Lu, X, Miao, X, Moore, B, Moorhead, M, Namsaraev, E, Pasternak, S, Prakash, E, Tran, K, Wang, Z, Jones, HB, Davis, RW, Willis, TD, Gibbs, RA
JournalGenome Res
Volume15
Issue2
Pagination269-75
Date Published2005 Feb
ISSN1088-9051
KeywordsChromosome Inversion, Cluster Analysis, DNA Probes, Gene Expression Profiling, Genome, Human, Genotype, Humans, Molecular Probe Techniques, Molecular Probes, Polymorphism, Single Nucleotide, Research Design
Abstract

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 approximately 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.

DOI10.1101/gr.3185605
Alternate JournalGenome Res.
PubMed ID15687290
PubMed Central IDPMC546528
Grant ListU54 HG002755 / HG / NHGRI NIH HHS / United States
1U54HG02755 / HG / NHGRI NIH HHS / United States