Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline.
Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline.
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DOI：
10.1016/j.humimm.2015.12.006
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发表时间：
2016-03
期刊：
影响因子：
2.7
通讯作者：
Mack SJ
中科院分区：
文献类型：
--
作者：
Pappas DJ;Marin W;Hollenbach JA;Mack SJ
弥合免疫基因组数据分析工作流程差距 (BIGDAWG) 是一个集成的数据分析管道，旨在对高度多态性遗传数据（特别是 HLA 和 KIR 遗传系统）进行标准化分析。大多数现代遗传分析程序都是为分析单核苷酸多态性而设计的，但 HLA 和 KIR 数据的高度多态性需要专门的数据分析方法。 BIGDAWG 对 HLA 和 KIR 基因座的高度多态性基因型数据特征进行病例对照数据分析。 BIGDAWG 执行 Hardy-Weinberg 平衡检验，计算 k × 2 和 2 × 2 卡方检验的等位基因频率和低频等位基因箱，并计算每个等位基因的优势比、置信区间和 p 值。当多位点基因型数据可用时，BIGDAWG 估计用户指定的单倍型，并对每个单倍型执行相同的分箱和统计计算。对于 HLA 基因座，BIGDAWG 在单个氨基酸水平上进行相同的分析。最后，BIGDAWG 为每个比较生成图表。 BIGDAWG 避免了在多个程序之间传输数据所需的容易出错的重新格式化，并简化和标准化了高度多态性数据的病例对照研究的数据分析过程。 BIGDAWG 已作为 bigdawg R 包和 bigdawg.immunogenomics.org 上的免费 Web 应用程序实现。
Bridging ImmunoGenomic Data-Analysis Workflow Gaps (BIGDAWG) is an integrated data-analysis pipeline designed for the standardized analysis of highly-polymorphic genetic data, specifically for the HLA and KIR genetic systems. Most modern genetic analysis programs are designed for the analysis of single nucleotide polymorphisms, but the highly polymorphic nature of HLA and KIR data require specialized methods of data analysis. BIGDAWG performs case-control data analyses of highly polymorphic genotype data characteristic of the HLA and KIR loci. BIGDAWG performs tests for Hardy-Weinberg equilibrium, calculates allele frequencies and bins low-frequency alleles for k × 2 and 2 × 2 chi-squared tests, and calculates odds ratios, confidence intervals and p-values for each allele. When multi-locus genotype data are available, BIGDAWG estimates user-specified haplotypes and performs the same binning and statistical calculations for each haplotype. For the HLA loci, BIGDAWG performs the same analyses at the individual amino-acid level. Finally, BIGDAWG generates figures and tables for each of these comparisons. BIGDAWG obviates the error-prone reformatting needed to traffic data between multiple programs, and streamlines and standardizes the data-analysis process for case-control studies of highly polymorphic data. BIGDAWG has been implemented as the bigdawg R package and as a free web application at bigdawg.immunogenomics.org.