Identification of 9p and 20q Germline Alterations in Glioblastoma Pathogenesis

描述(由申请人提供)：本申请涉及广泛的挑战领域(08)基因组学，以及特定的挑战主题08-CA-101*加强全基因组关联研究。胶质母细胞瘤(GBM)的发展被认为与相对常见的外显性有限的生殖系改变有关。最近，我们与加州大学旧金山分校(UCSF)的研究小组合作，报道了映射到9P和20Q的SNP与GBM的发生有关。我们建议表征这些9P和20Q区域内的胚系改变，并将这些变化与胶质瘤9P缺失和20Q增加相关联。具体目标1：使用1200例病例和对照对相关的9P和20Q区域进行详细的种系遗传分析，以确定已知多态和新变化的患病率。目的1a：对600例既往基因分型病例和所有非冗余SNP的配对对照进行定制的基因分型，以更好地确定单倍型。归因于单倍型，并评估其与GBM发育的相关性。目的1b：对携带高危单倍型的50例GBM患者和50例对照分别进行~200kb和~100kb区域9p和~100kb高通量测序。为了直接确定单倍型结构，对50个分离的高危和非高危染色体进行高通量测序。目的1c：在600例新病例和配对对照中定制候选基因多态，以验证AIMS 1a和1b的新变化。目的1D：对9p和20q区域进行定制的aCGH分析，以确定拷贝数变异。具体目标2：对病例中的胶质瘤进行详细的基因分析和表达分析。目的2a：使用FISH和定制CGHa定义胶质瘤9P缺失和20Q增加状态。目的2b：对9p和20q区域的所有外显子进行测序。评估目标基因启动子的甲基化。目的2c：研究靶区内所有已知外显子和miRNAs在肿瘤中的表达。确定潜在的GBM基因亚型。具体目标3：将多态/改变/单倍型患病率差异与获得性胶质瘤改变相关联，以生成可能与胶质瘤发展相关的候选种系9P和20Q突变列表。胶质瘤会导致严重的发病率和死亡率。在美国，每年大约有18,500人被诊断出患有胶质瘤。由于大多数胶质瘤具有生物学侵袭性，美国每年约有12,800人死于这种肿瘤。了解脑胶质瘤的易感性，对于脑胶质瘤的预防和治疗具有重要意义。

DESCRIPTION (provided by the applicant): This application addresses broad Challenge Area (08) Genomics, and specific Challenge Topic 08-CA-101* Augmenting Genome-Wide Association Studies. The development of glioblastoma (GBM) has been hypothesized to be associated with relatively common germline alterations with limited penetrance. Collaborating with the group at the University of California at San Francisco (UCSF) we recently reported that SNPs mapping to 9p and 20q are associated with the development of GBM. We propose to characterize the germline alterations within these 9p and 20q regions and to correlate these with glioma 9p deletion and 20q gain. Specific Aim 1: Perform detailed germline genetic analysis of the associated 9p and 20q regions using 1200 cases and controls to determine the prevalence of known polymorphisms and new alterations. Aim 1a: Perform custom genotyping of 600 previously genotyped cases and matched controls for all non-redundant SNPs to better define haplotypes. Impute haploytpes and evaluate their association with GBM development. Aim 1b: Perform high-throughput sequencing of the ~200kb and ~100kb regions within 9p and 20, respectively, in 50 GBM cases and 50 controls that carry the imputed at-risk haplotypes. To directly determine haplotype structure, perform high-through-put sequencing of 50 isolated at-risk and non-risk chromosomes. Aim 1c: Custom genotype candidate polymorphisms in 600 new cases and matched controls to validate new alterations from Aims 1a and 1b. Aim 1d: Perform custom aCGH analysis of the 9p and 20q regions to ascertain copy number variants. Specific Aim 2: Perform detailed genetic analysis and expression analysis of gliomas from the cases. Aim 2a: Using FISH and custom CGHa define glioma 9p deletion and 20q gain status. Aim 2b: Sequence all exons in the 9p and 20q regions. Assess methylation of target gene promoters. Aim 2c: Evaluate the tumor expression of all known exons and miRNAs within the targeted regions. Determine the underlying GBM genetic subtype. Specific Aim 3: Correlate polymorphism/ alteration/haplotype prevalence differences and with acquired glioma alterations to generate a list of candidate germline 9p and 20q mutations likely to be associated with the development of gliomas. Gliomas cause significant morbidity and mortality. Approximately 18,500 people in the U.S. are diagnosed with glioma each year. Because most gliomas are biologically aggressive, approximately 12,800 people in the U.S. succumb to these tumors every year. Understanding the predisposition to gliomas will have major implications for the prevention of gliomas as well as the management of these tumors.