Association Mapping in PD Linkage Regions

连锁分析是一个强有力的工具，以确定导致疾病的基因。使用这种方法，我们以前确定了5个区域，在染色体5，6，8，9和17（斯科特等2001），可能含有PD风险基因。独立基因组筛选的最新结果现在已经复制了我们与5号和9号染色体的联系。我们已经证明了6号染色体区域是由于帕金基因突变和后续的17号染色体上确实检测到PD和H1与tau基因相关的单倍型之间的关联。我们现在与8号染色体上的一个基因也有显著的关联，支持这种联系。然而，复杂疾病中的连锁峰提出了几个新的问题， 试图用这种方法来鉴定致病基因。首先，连锁峰非常大，通常为20 - 30兆碱基（Mb）或更多。这就产生了一个巨大的需求，即以一种具有成本效益和节省劳动力的方法来优先考虑候选基因，这在一定程度上导致了我们的基因组融合方法。第二，在囊性纤维化等疾病的终点是基因突变的情况下，在复杂疾病中，连锁分析的终点是鉴定具有"显著"疾病关联的era基因。但有多重要？我们怎么知道一个显著相关的基因实际上就是产生连锁结果的基因呢？在这个区域中，是否有一个更重要的基因，但尚未被探索，是人们正在寻找的实际基因？此外，是否只有一种关联对这些峰值有贡献？该项目建议采用基因组方法来回答这个问题。我们将应用DNA池化策略（Hoogendoom et al.1999），使用单碱基对延伸 与变性高效液相色谱应用一种新的技术，"迭代关联映射"（IAM）的整个连锁峰在一个有效的方式。然后，我们将专注于最强，最主要的关联峰，从合并到基因分型（Taqman），以在小测试集上识别单倍型标记SNP，然后在完整数据集上对htSNP进行基因分型。最后，我们将测试位于相关htSNP区域的基因与PD的关联。

Linkage analysis is a powerful tool to identify the genes that lead to disease. Using this approach, we previously identified five regions, on chromosomes 5, 6, 8, 9 and 17 (Scott et al. 2001) that potentially contained PD risk genes. Recent results from independent genomic screens have now replicated our linkages to chromosomes 5 and 9. We have demonstrated the chromosome 6 region was due to Parkin gene mutations and follow-up on chromosome 17 indeed detected association between PD and the H1 haplotype associated with the tau gene. We now have significant association with a gene on chromosome 8 as well, supporting this linkage. However, linkage peaks in complex diseases present several new problems when attempting to use this method to identify the causal gene. First, the linkage peaks are very large, often 20-30 megabases (Mb) or more. This creates a great need for prioritizing candidate genes in a cost-effective and labor-saving approach, which led in part to our genomic convergence approach. Second, where the endpoint of a disorder like cystic fibrosis is a gene mutation, in complex diseases the endpoint of linkage analysis is identification era gene with "significant" disease association. But how significant? How does one know that a significantly associated gene is actually the gene producing the linkage result? Could a more important gene in the region, yet unexplored, be the actual gene that one is seeking? Also, is only one association contributing to these peaks? This project proposes to take a genomic approach to answer this question. We will apply a DNA pooling strategy (Hoogendoom et al. 1999) using single base-pair extension with denaturing high performance liquid chromatography to apply a new technique, "iterative association mapping" (IAM) to the entire linkage peak in an efficient manner. We will then focus on the strongest, most dominant peak of association, move from pooling to genotyping (Taqman) to identify haplotype-tagging SNPs on a small test set, then genotype the htSNPs on the full data set. Finally, we will test genes lying in the associated htSNP region for association with PD.