Tobler Andreas R, Short Sabine, Andersen Mark R, Paner Teodoro M, Briggs Jason C, Lambert Stephen M, Wu Priscilla P, Wang Yiwen, Spoonde Alexander Y, Koehler Ryan T, Peyret Nicolas, Chen Caifu, Broomer Adam J, Ridzon Dana A, Zhou Hui, Hoo Bradley S, Hayashibara Kathleen C, Leong Lilley N, Ma Congcong N, Rosenblum Barnet B, Day Joseph P, Ziegle Janet S, De La Vega Francisco M, Rhodes Michael D, Hennessy Kevin M, Wenz H Michael
Applied Biosystems, Foster City, CA 94404, USA.
J Biomol Tech. 2005 Dec;16(4):398-406.
We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.
我们开发了SNPlex基因分型系统，以满足对准确基因分型数据、高样本通量、研究设计灵活性和成本效益的需求。该系统使用寡核苷酸连接/聚合酶链反应和毛细管电泳来分析双等位基因单核苷酸多态性基因型。它非常适合那些通量和成本效益至关重要的单核苷酸多态性基因分型工作。SNPlex基因分型系统具有高度的灵活性和可扩展性，允许为中高通量基因分型项目选择定制的单核苷酸多态性集合。因此，它适用于广泛的研究设计。在本文中，我们描述了SNPlex基因分型系统的原理和应用，以及一组加速检测设计过程的单核苷酸多态性选择工具和经过验证的检测资源。我们开发了对照池，这是一组用于训练和质量控制目的的寡核苷酸连接探针，可同时检测48个单核苷酸多态性。我们展示了通过检测44个个体的基因组DNA样本从该对照池中获得的性能数据。此外，我们展示了一项对92个个体中的521个单核苷酸多态性进行分析的研究数据。两项研究综合表明，SNPlex基因分型系统的总体检出率为99.32%，精度为99.95%，与基于TaqMan探针的检测分析的基因型一致性为99.84%。SNPlex基因分型系统是一种高效可靠的工具，适用于广泛的基因分型应用，并得到研究设计、数据分析和数据管理应用的支持。
