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) 基因组学和特定挑战主题 08-CA-101* 增强全基因组关联研究。据推测，胶质母细胞瘤（GBM）的发展与相对常见的外显率有限的种系改变有关。我们最近与加州大学旧金山分校 (UCSF) 的研究小组合作，报告了映射到 9p 和 20q 的 SNP 与 GBM 的发展相关。我们建议表征这些 9p 和 20q 区域内的种系改变，并将这些改变与神经胶质瘤 9p 缺失和 20q 增益相关联。具体目标 1：使用 1200 个病例和对照对相关 9p 和 20q 区域进行详细的种系遗传分析，以确定已知多态性和新变异的患病率。目标 1a：对 600 个先前基因分型的病例和所有非冗余 SNP 的匹配对照进行定制基因分型，以更好地定义单倍型。估算单倍型并评估它们与 GBM 发育的关联。目标 1b：分别在 50 个 GBM 病例和 50 个携带推算高危单倍型的对照中，对 9p 和 20 内的 ~200kb 和 ~100kb 区域进行高通量测序。为了直接确定单倍型结构，对 50 条分离的风险和非风险染色体进行高通量测序。目标 1c：在 600 个新病例中定制基因型候选多态性并匹配对照，以验证目标 1a 和 1b 的新改变。目标 1d：对 9p 和 20q 区域进行定制 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遗传分析和表达分析。目标 2a：使用 FISH 和定制 CGHa 定义神经胶质瘤 9p 缺失和 20q 增益状态。目标 2b：对 9p 和 20q 区域中的所有外显子进行测序。评估靶基因启动子的甲基化。目标 2c：评估目标区域内所有已知外显子和 miRNA 的肿瘤表达。确定潜在的 GBM 遗传亚型。具体目标 3：将多态性/改变/单倍型患病率差异与获得性神经胶质瘤改变相关联，以生成可能与神经胶质瘤发展相关的候选种系 9p 和 20q 突变列表。神经胶质瘤导致显着的发病率和死亡率。美国每年约有 18,500 人被诊断患有神经胶质瘤。由于大多数神经胶质瘤具有生物学侵袭性，因此美国每年约有 12,800 人死于这些肿瘤。了解神经胶质瘤的易感性将对神经胶质瘤的预防以及这些肿瘤的治疗产生重大影响。

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.