Complete Genome Variation in Africans with Extreme HIV-1 Transmission Phenotypes

说明(申请人提供)：解释自然宿主对HIV-1感染的抵抗力(尽管有广泛的性接触但仍未感染的人)的挑战仍未完全解决。虽然已经确定了一些影响对艾滋病毒-1感染的自然抵抗力的宿主遗传变异，但很少在非洲人群(受这一大流行影响最大的人群)中进行这种研究，也没有在任何人群中进行全面的全基因组评估，以捕捉影响艾滋病毒-1感染的常见和低频宿主遗传变异。其中一个原因是，此类研究必须控制影响HIV-1暴露风险的流行病学因素(例如，感染方的血浆HIV-1水平，以及未感染方的男性包皮环切状况)。这些暴露数据必须从感染艾滋病毒-1的性伴侣和未感染艾滋病毒-1的性伴侣那里收集，从而有必要招募艾滋病毒-1血清不一致的夫妇(一个伴侣感染艾滋病毒-1，另一个没有感染)--这是一项昂贵而复杂的研究设计。在过去的6年里，在进行2项艾滋病毒-1预防临床试验和一项观察性研究的过程中，我们招募了3大批非洲艾滋病毒-1血清不一致的异性恋夫妇，包括近8,600对夫妇(17,200人)，每对夫妇每月或每季度随访12至36个月，以评估最初未感染艾滋病毒-1的伴侣中艾滋病毒-1血清转换的情况。这些队列的中央标本库位于华盛顿大学，目前保存着100多万份广泛的临床样本类型，包括用于基因组研究的全血。还从所有参与者那里收集了流行病学、临床和行为数据，以便详细评估影响艾滋病毒-1传播风险的艾滋病毒-1暴露因素。在这里，我们建议使用这一独特的现有标本和数据存储库和“下一代”DNA测序技术，对影响HIV-1传播的宿主基因组因素进行全面分析。为了广泛捕捉宿主遗传风险因素，我们建议对50名感染HIV-1并低水平暴露于HIV-1的个体和50名尽管高异性暴露于该病毒但仍对HIV-1感染具有抵抗力的个体的基因组进行完整测序。这种极端的表型方法将最大限度地提高我们捕获与HIV-1传播相关的宿主遗传因素的能力。然后，将在剩余的队列中对从这些序列数据中确定的一组高优先级变异进行基因分型，以确定非洲人中与自然宿主易感性和对艾滋病毒-1传播的抵抗力有关的宿主遗传变异。这些数据可以提供关键的见解，特别是对于开发艾滋病毒-1预防干预措施(例如疫苗佐剂或基因表达调节剂)，以广泛地诱导宿主对艾滋病毒-1感染的抵抗力。

DESCRIPTION (provided by applicant): The challenge of explaining natural host resistance to HIV-1 infection (individuals who remain uninfected despite extensive sexual exposure to the virus) remains incompletely addressed. While some host genetic variants that influence natural resistance to HIV-1 infection have been identified few such studies have been conducted in cohorts of Africans (who are most impacted by this pandemic), and no comprehensive genome-wide evaluation that captures common and low-frequency host genetic variation influencing HIV-1 infection has been done in any population. One reason for this is that such studies must control for epidemiologic factors (e.g., level of plasma HIV-1 in the infected parter, and male circumcision status in the uninfected partner) that modify HIV-1 exposure risk. These exposure data must be collected from both the HIV-1 infected and HIV-1 uninfected sexual partner necessitating recruitment of HIV-1 serodiscordant couples (one partner HIV-1 infected and the other uninfected) - a costly and complex study design. Over the past 6 years, in the course of conducting 2 HIV-1 prevention clinical trials and an observational study, we have recruited 3 large cohorts of African HIV-1 serodiscordant heterosexual couples encompassing nearly 8,600 couples (17,200 individuals) each with 12 to 36 months of monthly or quarterly follow-up to evaluate for HIV-1 seroconversion in the initially HIV-1 uninfected partner. The central specimen repository for these cohorts is located at the University of Washington and currently holds over a million aliquots of a wide range of clinical sample types including whole blood for genomic studies. Epidemiologic, clinical and behavioral data have also been collected from all participants permitting detailed evaluation of HIV- 1 exposure factors affecting risk of HIV-1 transmission. Here we propose to use this unique existing specimen and data repository and "next generation" DNA sequencing technology to perform a comprehensive analysis for host genomic factors affecting HIV-1 transmission. In order to broadly capture host genetic risk factors, we propose to completely sequence the genomes of 50 individuals who became HIV-1 infected with low levels of HIV-1 exposure and 50 individuals resistant to HIV-1 infection despite high levels of heterosexual exposure to the virus. This extreme phenotype approach will maximize our power to capture host genetic factors associated with HIV-1 transmission. A set of high priority variants identified from these sequence data will then be genotyped in the remaining cohort to identify host genetic variants in Africans associated with natural host susceptibility and resistance to HIV-1 transmission. These data could provide critical insights particularly toward developing HIV-1 prevention interventions (e.g. vaccine adjuvants or gene expression modulators) to broadly elicit host resistance to HIV-1 infection.