Resequencing and Functional Studies to Identify Causal Gene Variants of Lymphoma

描述（由申请人提供）：非霍奇金淋巴瘤（NHL）是美国第五大常见癌症，也是全球排名第一的血液恶性肿瘤。NHL对发病率和死亡率有重大影响；因此，能够识别致病基因变异的研究将有助于通过更好的筛查来识别高危个体；提供重要的线索，以确定可能适合治疗调节的生物学途径/靶点；并为淋巴瘤研究提供新的研究方向。为了实现这一目标，基于全基因组关联研究对已知与NHL相关的目标基因组区域进行重测序，然后在大型、表型良好的研究中（如在一个联合体中）验证潜在的因果snp是至关重要的，这将有助于建立真正的因果遗传变异。进一步表征因果基因变异也是至关重要的。两例NHL的GWAS结果显示，主要组织相容性复合体（MHC）区域6p21.32-33染色体带snp和HLA等位基因与NHL主要亚型之一滤泡性淋巴瘤（FL）的发病风险相关。我们的GWAS表明，FL存在重要的遗传作用。MHC区域先前与一些自身免疫性疾病有关，表明它们可能与FL具有共同的风险等位基因。InterLymph成员研究已经确定了其他易感位点，其中一些位于MHC之外，已在联盟中得到验证。因此，由于尚未对此类淋巴瘤进行研究，因此有强烈的动力来确定已知影响FL和其他NHL亚型风险的因果基因变异。为了实现这一目标，将实现以下目标：在目标1中，将实施靶向DNA捕获和下一代测序，以确定MHC和与FL相关的其他区域的所有基因变异（罕见和常见的snp和结构变异）。DNA已经从两个大型基于人群的NHL病例对照研究中提取。一旦在研究人群中发现了新的和已知的snp并测试了与FL的关联，将进行计算机功能分析来预测因果snp。在目标2中，假定功能性snp将在NHL流行病学研究国际研究人员联盟（InterLymph）的独立病例对照研究中进行基因分型。在Aim 3中，将评估非洲裔美国人FL病例的HLA等位基因和snp，以帮助解决MHC内欧洲人群的高LD问题。在Aim 4中，验证的snp将被功能表征。越来越多的证据支持遗传变异在MHC中与许多自身免疫性疾病风险的作用。因此，鉴定该区域淋巴瘤的致病基因变异也可能有助于了解其他具有共同易感位点的疾病。

DESCRIPTION (provided by applicant): Non-Hodgkin lymphoma (NHL) is the fifth most common cancer in the U.S. and the number one hematological malignancy worldwide. NHL has a major impact on morbidity and mortality; thus, studies that lead to the identification of causal gene variants will help to identify at-risk individuals through better screening; provide important clues to identify biological pathways/targets that may be amenable to therapeutic modulation; and provide new directions for studies that benefit lymphoma research. To accomplish this, resequencing targeted genomic regions known to be associated with NHL based on genome-wide association studies, followed by validation of potentially causal SNPs in large, well-phenotyped studies (such as in a consortium) is of utmost importance and will help to establish true causal genetic variants. Further characterization of causal gene variants is also crucial. Based on findings from two GWAS of NHL, SNPs and HLA alleles on chromosome band 6p21.32-33 in the major histocompatibility complex (MHC) region were associated with risk of follicular lymphoma (FL), one of the major subtypes of NHL. Our GWAS suggests an important genetic role exists for FL. MHC regions have been previously linked to some autoimmune disorders suggesting that they may share common risk alleles with FL. InterLymph member studies have identified additional susceptibility loci, some outside of the MHC, that have been validated within the consortium. Thus, there is a strong impetus to identify causal gene variants known to affect risk of FL and other NHL subtypes since no studies of this kind for lymphoma have been performed. To accomplish this, the following Aims will be undertaken: In Aim 1, targeted DNA capture and next generation sequencing will be implemented to identify all gene variants (rare and common SNPs and structural variants) in the MHC and in other regions associated with FL. The DNA has already been extracted from two large population-based case-control studies of NHL. Once novel and known SNPs are identified and tested for association with FL in the study populations, in silico functional analysis will be undertaken to predict causal SNPs. In Aim 2, putatively functional SNPs will be genotyped in independent case-control studies within the International Consortium of Investigators Working on NHL Epidemiologic Studies (InterLymph). In Aim 3, HLA allelotypes and SNPs will be assessed in African-American FL cases to help address the issue of high LD in European populations within the MHC. In Aim 4, validated SNPs will be functionally characterized. Accumulating evidence supports the role of genetic variation in the MHC with risk of many autoimmune diseases. Thus, the identification of causal gene variants in this region for lymphoma may also prove helpful in understanding other diseases sharing common susceptibility loci. PUBLIC HEALTH RELEVANCE: Non-Hodgkin lymphoma (NHL) is the fifth most common cancer in the U.S and will account for over 66,000 newly diagnosed cases and 20,000 deaths in the U.S. and 300,000 cases and 175,000 deaths worldwide in 2010. We will perform genetic studies that will aid in the identification of common genetic variants that cause lymphoma. These studies will increase our understanding of how lymphoma develops in the body and provide new ways to screen, prevent and treat lymphoma.