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

TLDR

Large-scale genetic studies rely on efficient, scalable multiplex SNP assays. The authors developed a four‑color, single‑array Molecular Inversion Probe system capable of genotyping up to 12,000 SNPs per reaction. The method allows trade‑offs between conversion rate and accuracy, enabling high‑level accuracy without sacrificing throughput. Across 38,429 assays in 30 trios, the platform achieved ~90% conversion, >99.6% concordance, and >98% completeness at 12,000‑plex, with no loss of performance when scaling from 6,000 to 12,000‑plex, proving its suitability for large‑scale association studies.

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 ∼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.