Resequencing and Functional Studies to Identify Causal Gene Variants of Lymphoma

描述(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系统恶性肿瘤。非霍奇金淋巴瘤对发病率和死亡率有重大影响；因此，导致确定因果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；提供重要线索，以确定可能服从治疗调节的生物途径/靶点；并为有助于淋巴瘤研究的研究提供新的方向。要做到这一点，根据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新测序，然后在大型、表型良好的研究(如在联合体中)验证潜在的因果SNP是至关重要的，并将有助于建立真正的因果遗传变异。对因果基因变异的进一步表征也是至关重要的。根据两个非霍奇金淋巴瘤患者的研究结果，主要组织相容性复合体(MHC)区域染色体6p21.32-33的SNPs和HLA等位基因与NHL的主要亚型之一滤泡性淋巴瘤(FL)的风险相关。我们的GWAS表明FL存在重要的遗传作用。此前，MHC区域与一些自身免疫性疾病有关，这表明它们可能与FL具有共同的风险等位基因。InterLymph成员的研究已经确定了其他易感基因，其中一些在MHC之外，已经在该联盟内得到验证。因此，有一个强烈的动力，以确定已知的影响FL和其他非霍奇金淋巴瘤亚型风险的因果基因变异，因为还没有对淋巴瘤进行这类研究。为了实现这一目标，将实现以下目标：在目标1中，将实施有针对性的DNA捕获和下一代测序，以识别MHC和其他与FL相关的区域中的所有基因变异(罕见和常见的SNP和结构变异)。DNA已经从两项以人群为基础的NHL病例对照研究中提取出来。一旦在研究人群中发现了新的和已知的SNPs，并测试了其与FL的关联，就将进行功能分析来预测因果SNPs。在目标2中，假定有功能的SNPs将在国际非霍奇金淋巴瘤流行病学研究(InterLymph)研究人员国际联合会内的独立病例对照研究中进行基因分型。在目标3中，将评估非裔美国人FL病例中的人类白细胞抗原等位基因和SNPs，以帮助解决MHC中欧洲人群中的高LD问题。在目标4中，将对经过验证的单核苷酸多态进行功能性描述。越来越多的证据支持遗传变异在具有许多自身免疫性疾病风险的MHC中所起的作用。因此，识别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基因的疾病。

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.