New Familial Colon Cancer Gene Discovery Via Combined Linkage and SNP Association

通过联合连锁和 SNP 关联发现新的家族性结肠癌基因

• 批准号: 8533989
• 负责人: SANFORD D. MARKOWITZ
• 金额: $ 10.74万
• 依托单位: CASE WESTERN RESERVE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-07-25 至 2013-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8533989
• 关键词: APC gene; Accounting; Adenomatous Polyposis Coli; Adult; Affect; Age; Alleles; American; British; Cancer Cluster; Cancer Etiology; Cancer Patient; Candidate Disease Gene; Cessation of life; Chromosome Mapping; Chromosomes; Chromosomes, Human, Pair 9; Colon Carcinoma; Colonic Adenoma; Colonic Neoplasms; Colorectal Cancer; DNA; Development; Disease; Disease Association; Dysplasia; Early Diagnosis; Enrollment; Exons; Family; Family Study; Family history of; First Degree Relative; Gene Dosage; Gene Mutation; Gene Structure; Genes; Genetic; Genetic Markers; Genetic Polymorphism; Genetic Variation; Genome Scan; Genomics; Germ-Line Mutation; Goals; Haploidy; Health; Hereditary Nonpolyposis Colorectal Neoplasms; Histologic; Histology; Human; Human Cloning; Hybrid Cells; Individual; Inherited; Life; Link; Linkage Disequilibrium; Location; Loss of Heterozygosity; Malignant Neoplasms; Maps; Methods; Mismatch Repair; Mus; Mutation; Oncogenes; Parents; Pattern; Population; Predisposition; Public Health; Reporting; Research Personnel; Risk; Scandinavia; Scandinavian; Screening procedure; Siblings; Syndrome; Techniques; Testing; Transcript; Tumor Suppressor Genes; United States; Variant; base; cancer risk; cohort; design; disease-causing mutation; early onset; exon skipping; falls; gene discovery; genetic linkage; genetic linkage analysis; genome wide association study; high risk; high standard; improved; kindred; mutant; novel; success; tumor

DESCRIPTION (provided by applicant): Our group of investigators has identified and confirmed a novel chromosomal region, 9q22.2-31.2, that demonstrates evidence for linkage (P=0.00016) to familial colon neoplasia in a pattern consistent with dominant autosomal disease alleles in this region accounting for an estimated 40% of colon cancers and advanced colon adenomas in the colon neoplasia families we studied. Our initial finding was the result of linkage analysis of a sibling pair study that was designed to identify novel human colon cancer susceptibility loci based on an unbiased whole genome scan employing sibling pairs drawn from 53 "study-4" kindreds in which 2 or more siblings had by age 65 or younger been affected by colon cancer, or affected by advanced colon adenomas (of size >1cm or with histology demonstrating high grade dysplasia) that are direct cancer precursors. Our initial discovery has now been confirmed by us in an enlarged cohort of 120 "study-4" kindreds, as well by independent investigators in Britain and in Scandinavia. After fine mapping, our currently refined linkage region spans 8.8Mb. The main purpose of this new proposal is to further narrow this candidate region using non-linkage based techniques, such as i) SNP association, and ii) mapping gene regions that familial tumors target for loss {or for gains}; followed by then identifying the actual novel disease gene and pathogenetic disease alleles within the 9q22.2-31.2 interval. The specific steps we thus now propose are: i) To analyze the 9q22.2-31.2 interval for evidence of either a tumor suppressor gene {or an oncogene} by examining this interval for, respectively, either loss of heterozygosity (LOH) {or for increased gene copy number} in the tumors arising in kindreds that show linkage to the region. To then further narrow this genomic interval by defining the minimal region of LOH {or of increased gene copy number} that is shared in common among these familial colon tumors. ii) To examine disease association among {a comprehensive panel of 5147 SNP polymorphisms, with average spacing of average 2.7kb, that capture both the common and the rare genetic variation across the 9q22.2-31.2 linkage interval;} thereby directly or indirectly mapping the location of any potential founder disease allele that would account for tumor development in many or all of these colon neoplasia families. iii) To directly look for potential disease genes and pathogenetic disease alleles by studying our best linked kindreds via high throughput sequencing of all genes within our maximally narrowed 9q22.2-31.2 interval, examining a maximum of 102 genes contained within our currently narrowed 8.8Mb linkage interval. iv) To in our best linked families construct "converted clone" human-mouse somatic cell hybrids to capture individual parental human chromsome 9 copies. To employ these captured haploid parental chromsomes to test the genes in our maximally narrowed interval for disease causing mutations that would not be detected by standard approaches, including testing for exon deletions and testing for mutations that cause exon skipping. Success of this project would have substantial implications for public health. PUBLIC HEALTH RELEVANCE: Colon cancer is the second leading cause of cancer death in the United States, with 20% of colon cancer patients reporting a positive family history of colon cancer also affecting either a parent or sibling. Identifying a new gene that is a common cause of familial colon cancer would allow identification of individuals at high risk for this disease, for whom aggressive screening and early detection could be life saving.

描述（由申请人提供）：我们的研究小组已鉴定并确认了一个新的染色体区域 9q22.2-31.2，该区域证明了与家族性结肠肿瘤相关的证据（P = 0.00016），其模式与显性常染色体疾病等位基因一致。在我们研究的结肠肿瘤家族中，该区域估计占结肠癌和晚期结肠腺瘤的 40%。我们最初的发现是一项兄弟姐妹对研究的连锁分析结果，该研究旨在基于无偏倚的全基因组扫描来识别新的人类结肠癌易感位点，该扫描采用来自 53 个“研究 4”亲属的兄弟姐妹对，其中有 2 个或更多兄弟姐妹65 岁或以下曾患有结肠癌，或患有直接癌症前兆的晚期结肠腺瘤（大小 >1 厘米或组织学显示高度异型增生）。我们最初的发现现已在 120 个“study-4”亲属的扩大队列中得到证实，英国和斯堪的纳维亚半岛的独立研究人员也证实了这一点。经过精细映射后，我们当前细化的链接区域跨度为 8.8Mb。这项新提案的主要目的是使用基于非连锁的技术进一步缩小该候选区域，例如 i) SNP 关联，以及 ii) 绘制家族性肿瘤靶向损失（或增益）的基因区域；然后确定9q22.2-31.2区间内的实际新疾病基因和致病等位基因。因此，我们现在提出的具体步骤是： i) 通过分别检查该区间的杂合性丢失（LOH）{或增加的基因拷贝数}在与该区域有联系的亲属中产生的肿瘤中。然后，通过定义这些家族性结肠肿瘤共有的 LOH（或增加的基因拷贝数）的最小区域，进一步缩小该基因组区间。 ii) 检查{5147个SNP多态性的综合面板，平均间距为2.7kb，捕获9q22.2-31.2连锁区间的常见和罕见遗传变异；}从而直接或间接绘制图谱任何潜在的始祖疾病等位基因的位置，该等位基因将解释许多或所有这些结肠瘤形成家族中肿瘤的发展。 iii) 通过对我们最大缩小的 9q22.2-31.2 区间内的所有基因进行高通量测序来研究我们的最佳连锁亲属，从而直接寻找潜在的疾病基因和致病等位基因，检查我们目前缩小的 8.8Mb 内包含的最多 102 个基因联动间隔。 iv) 在我们最好的连锁家族中构建“转化克隆”人-小鼠体细胞杂交体以捕获个体亲本人染色体9拷贝。利用这些捕获的单倍体亲本染色体来测试我们最大程度缩小的间隔内的基因，以检测标准方法无法检测到的致病突变，包括检测外显子缺失和检测导致外显子跳跃的突变。该项目的成功将对公众健康产生重大影响。公共卫生相关性：结肠癌是美国癌症死亡的第二大原因，20% 的结肠癌患者报告其父母或兄弟姐妹也有结肠癌阳性家族史。识别出家族性结肠癌常见原因的新基因将能够识别出患有这种疾病的高风险个体，对他们来说积极的筛查和早期检测可能会挽救生命。