Analysis of high-density single-nucleotide polymorphism data: three novel methods that control for linkage disequilibrium between markers in a linkage analysis.
Analysis of high-density single-nucleotide polymorphism data: three novel methods that control for linkage disequilibrium between markers in a linkage analysis.
复制标题
DOI：
10.1186/1753-6561-1-s1-s160
复制
发表时间：
2007
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
我们使用6号染色体和21号染色体的高密度单核苷酸多态性（SNP）数据，使用遗传分析车间15 （GAW15）数据，对类风湿关节炎（RA）进行了多点连锁分析。这些区域先前被证明具有较高的LOD分数，但没有解释连锁不平衡（LD）。我们提出了三种在连锁分析中控制LD的新方法：使用图形建模允许标记之间的LD，使用单倍型数据通过主成分分析（PCA）消除高LD标记，以及使用基因型数据通过PCA消除高LD标记。将这三种新方法与先前发表的SNPLINK高ld消除方法进行了比较。虽然这四种方法都验证了之前的结果，但观察到不同方法之间连锁峰高度和位置的差异。需要进一步的工作来进一步了解LD对连接结果的影响，并探索LD控制方法。
We performed a multipoint linkage analysis for rheumatoid arthritis (RA) using high-density single-nucleotide polymorphism (SNP) data for chromosome 6 and chromosome 21 using Genetic Analysis Workshop 15 (GAW15) data. These regions were previously shown to have high LOD scores, not accounting for linkage disequilibrium (LD). We propose three novel methods to control for LD in a linkage analysis: allow for LD between markers using graphical modeling, eliminate high-LD markers by principal-component analysis (PCA) using haplotype data, and eliminate high-LD markers by PCA using genotype data. All three novel methods were compared to the previously published SNPLINK high-LD elimination method. Although all four methods verified the previous results, differences in linkage peak height and position were observed across methods. Additional work is required to further understand the effects of LD on linkage results and explore LD control methodology.