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）：我们的研究小组已经发现并证实了一个新的染色体区域9q22.2-31.2，该区域与家族性结肠肿瘤的关联（P=0.00016）与该区域的显性常染色体疾病等位基因的模式一致，在我们研究的结肠肿瘤家族中，该区域约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，该研究旨在通过无偏全基因组扫描确定新的人类结肠癌易感位点，该研究采用来自53个“study-4”家族的兄弟姐妹对，其中2个或更多的兄弟姐妹在65岁或65岁以下患有结肠癌，或患有晚期结肠癌腺瘤（大小为bbb1cm或组织学表现为高度发育不良），这些都是直接的癌症前兆。我们最初的发现现在已经得到了我们的证实，我们对120个“研究4”家族的扩大队列进行了研究，英国和斯堪的纳维亚半岛的独立调查员也证实了这一点。经过精细映射，我们目前提炼的联动区域跨度为8.8Mb。这项新提议的主要目的是使用非连锁技术进一步缩小这一候选区域，例如i) SNP关联，以及ii)定位家族性肿瘤靶向的基因区域以损失{或获得}；然后鉴定9q22.2-31.2区间内的实际新发疾病基因和致病疾病等位基因。因此，我们现在提出的具体步骤是：i)分析9q22.2-31.2区间，通过分别检查与该区域有连锁关系的种类中所产生的肿瘤的杂合性缺失（LOH）{或基因拷贝数增加}，来寻找肿瘤抑制基因{或致癌基因}的证据。然后通过定义这些家族性结肠肿瘤共有的LOH（或基因拷贝数增加）的最小区域来进一步缩小这个基因组间隔。ii)检查5147个SNP多态性之间的疾病关联，平均间距为2.7kb，这些多态性捕获了9q22.2-31.2连锁区间内常见和罕见的遗传变异；从而直接或间接地绘制任何潜在的创始疾病等位基因的位置，这些等位基因可以解释许多或所有这些结肠肿瘤家族的肿瘤发展。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，研究我们最好的连锁类群，直接寻找潜在的疾病基因和致病疾病等位基因，在我们目前缩小的8.8Mb连锁区间内最多检测102个基因。iv)在我们最紧密联系的家庭中构建“转换克隆”人-鼠体细胞杂交体，以捕获亲本人类9号染色体的单个副本。利用这些捕获的单倍体亲本染色体，在我们最大限度地缩小的间隔内测试基因，以检测标准方法无法检测到的引起疾病的突变，包括检测外显子缺失和检测导致外显子跳变的突变。这一项目的成功将对公共卫生产生重大影响。公共卫生相关性：结肠癌是美国癌症死亡的第二大原因，20%的结肠癌患者报告有结肠癌家族史，也会影响父母或兄弟姐妹。确定家族性结肠癌的常见致病基因，将有助于确定患这种疾病的高危人群，对他们来说，积极的筛查和早期发现可能会挽救他们的生命。