Associating genetic variation to resistance to severe malaria in East Africa

描述（由申请人提供）：虽然现在已经确定了18种基因变异赋予对严重疟疾的抗性，主要是在西非，但只有一小部分在多项研究中得到了重复。在这里，我们建议评估罗人对疟疾的遗传易感性，这是一个来自种族背景的东非人群，与之前确定的大多数关联的人群非常不同。我们假设，确定影响疟疾易感性的遗传变异将导致新的药物靶点，但是迄今为止的一些候选变异可能不是真实的，因此需要复制。我们还建议通过对疟疾抗性基因的首次全基因组扫描来寻找新的易感性变异。该项目的第一阶段将进行疟疾易感性的重复研究。我们将研究539例罗罗病例和477例匹配对照中先前与疟疾耐药性相关的18种遗传变异。对于发生这些变异的9个基因，我们还将为罗人群体创建“单倍型图谱”，并确定所有频率为5%的单倍型，并评估其中是否有任何与疟疾抗性有关。这些基因的单倍型分析意义重大，因为它将使我们能够识别只存在于东非的新的风险变异，而东非的研究很少。第二阶段将是寻找与疟疾抗性相关的9个基因的自然选择历史。我们最近发表了一项协议，以寻找受自然选择影响的基因组区域。我们利用这一点来建立CD40配体和G6PD（两个先前与疟疾抗性相关的基因）选择的证据。我们现在建议使用相同的方案来寻找与东非人疟疾抗性相关的所有9个基因的自然选择证据。作为选择的第二个测试，我们还将比较卢奥人与马赛人抗疟疾单倍型的频率，马赛人和卢奥人一样起源于尼罗河，但历史上生活在低疟疾环境中。尽管罗人和马赛人有着相似的种族背景，但是发现的单倍型在频率上有很大的不同，这表明存在一种抗疟疾基因。第三阶段将进行疟疾抗性基因的试点全基因组扫描。以前与疟疾耐药性相关的所有基因都是通过“候选基因”方法确定的，在这种方法中，对少数被特别认为对疟疾发病机制有重要意义的基因进行了相关性测试。然而，一些最有趣的药物靶点可能存在于尚未测试的大量基因中。我们建议开展第一次全基因组关联扫描，以发现疟疾抗性基因，使用Affymetrix基因芯片技术扫描多达200名罗族严重疟疾病例、200名健康的罗族对照和100名健康的马赛人的5万个变体。我们不仅将搜索卢奥族病例和对照之间的频率差异，而且还将搜索卢奥族和马赛族之间频率显著不同的地区，尽管他们的种族起源相似，这表明在过去几千年里卢奥族的疟疾抗性选择。

DESCRIPTION (provided by applicant): Although 18 genetic variants have now been identified as conferring resistance to severe malaria, mostly in west Africans, only a subset have been replicated in multiple studies. Here we propose to assess genetic susceptibility to malaria in the Luo, an East African population from an ethnic background very different from the populations in which most of the associations were previously identified. We hypothesize that identifying genetic variation affecting susceptibility to malaria will lead to new drug targets, but that several of the candidate variants so far may not be real and thus need to be replicated. We also propose to search for new susceptibility variants, via the first whole-genome scan for malaria resistance genes. The first phase of this project will be to carry out a replication study for malaria susceptibility. We will study the 18 genetic variants previously associated to malaria resistance in 539 Luo cases and 477 matched controls. For the nine genes in which these variants occur, we will also create "haplotype maps" specific for the Luo population, and identify all the haplotypes of >5 percent frequency and assess whether any of them are associated to malaria resistance. The haplotype analysis in these genes is significant because it will allow us to identify new risk variants present only in East Africa, where few studies have been done. The second phase will be to search for a history of natural selection at nine genes associated with malaria resistance. We recently published a protocol to search for regions of the genome that have been affected by natural selection. We used this to establish evidence for selection at CD40 ligand and G6PD (two genes previously associated with malaria resistance). We now propose to use the same protocol to search for evidence of natural selection at all nine genes associated with malaria resistance in east Africans. As a second test for selection, we will also compare the frequencies of the malaria resistance haplotypes in the Luo to those in the Masai, a population that is also of Nilotic in origin like the Luo, but has historically lived in a low-malaria environment. The finding of a haplotype that is very different in frequency comparing the Luo and Masai, despite the similar ethnic background, would suggest the presence of a malaria resistance gene. The third phase will be to carry out a pilot whole-genome scan for malaria resistance genes. All the genes that were previously associated to resistance fo malaria were identified by the "candidate gene" approach, where a handful of genes that were specifically believed to be significant for malaria pathogenesis, were tested for association. However, it may be that some of the most interesting drug targets are in the mass of genes that have not yet been tested. We propose to carry out the first whole-genome association scan to find malaria resistance genes, using Affymetrix gene-chip technology to scan a panel of 50,000 variants in up to 200 Luo severe malaria cases, 200 healthy Luo controls, and 100 healthy Masai. We will search not only for differences in frequencies between Luo cases and controls, but also for regions that are strikingly different in frequency between the Luo and Masai despite their similar ethnic origin, suggesting selection for malaria resistance in Luo in the past few thousand years.