Orro Alessandro, Guffanti Guia, Salvi Erika, Macciardi Fabio, Milanesi Luciano
Consorzio Interuniversitario Lombardo per l'Elaborazione Automatica, Via Sanzio Raffaello 4, 20090 Segrate (MI), Italy.
BMC Bioinformatics. 2008 Mar 26;9 Suppl 2(Suppl 2):S13. doi: 10.1186/1471-2105-9-S2-S13.
Recent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of this large amount of genotypic data facilitates the whole genome search for genetic basis of diseases. We need a suitable information management system to efficiently manage the data flow produced by whole genome genotyping and to make it available for further analyses.
We have developed an information system mainly devoted to the storage and management of SNP genotype data produced by the Illumina platform from the raw outputs of genotyping into a relational database. The relational database can be accessed in order to import any existing data and export user-defined formats compatible with many different genetic analysis programs. After calculating family-based or case-control association study data, the results can be imported in SNPLims. One of the main features is to allow the user to rapidly identify and annotate statistically relevant polymorphisms from the large volume of data analyzed. Results can be easily visualized either graphically or creating ASCII comma separated format output files, which can be used as input to further analyses.
The proposed infrastructure allows to manage a relatively large amount of genotypes for each sample and an arbitrary number of samples and phenotypes. Moreover, it enables the users to control the quality of the data and to perform the most common screening analyses and identify genes that become "candidate" for the disease under consideration.
基因分型技术的最新进展使得能够为每个DNA样本使用数十万遗传标记生成高密度遗传图谱。如此大量的基因型数据的可得性促进了对疾病遗传基础的全基因组搜索。我们需要一个合适的信息管理系统来有效管理全基因组基因分型产生的数据流，并使其可用于进一步分析。
我们开发了一个信息系统，主要致力于将Illumina平台产生的SNP基因型数据从基因分型的原始输出存储和管理到关系数据库中。可以访问该关系数据库以导入任何现有数据并导出与许多不同遗传分析程序兼容的用户定义格式。在计算基于家系或病例对照的关联研究数据后，结果可以导入到SNPLims中。其主要特点之一是允许用户从大量分析数据中快速识别和注释具有统计学意义的多态性。结果可以很容易地以图形方式可视化或创建ASCII逗号分隔格式的输出文件，这些文件可以用作进一步分析的输入。
所提出的基础设施允许管理每个样本相对大量的基因型以及任意数量的样本和表型。此外，它使用户能够控制数据质量，并进行最常见的筛选分析，识别出成为所研究疾病“候选”的基因。
