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: 7664630
• 负责人: SANFORD D. MARKOWITZ
• 金额: $ 61.57万
• 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 2012-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7664630
• 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; 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; falls; gene discovery; genetic linkage; genetic linkage analysis; genome wide association study; high risk; high standard; improved; kindred; mutant; novel; public health relevance; 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鉴定并确认了一个新的染色体区域，9q22.2-31.2，其证明了与家族性结肠肿瘤的连锁（P=0.00016）证据，该连锁模式与该区域中占我们研究的结肠肿瘤家族中估计40%的结肠癌和晚期结肠腺瘤的显性常染色体疾病等位基因一致。我们最初的发现是一项同胞对研究的连锁分析的结果，该研究旨在基于无偏倚的全基因组扫描来鉴定新的人类结肠癌易感基因座，该扫描采用了从53个“研究-4”基因组中抽取的同胞对，其中2个或更多个同胞在65岁或更年轻时受到结肠癌的影响，或受作为直接癌症前体的晚期结肠腺瘤（大小>1cm或组织学显示高度异型增生）影响。我们最初的发现现在已经被我们在一个扩大的120个“研究-4”kinematic队列中证实，以及被英国和斯堪的纳维亚的独立研究人员证实。经过精细定位，我们目前细化的连锁区域跨越8.8Mb。该新提议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，和ii）定位家族性肿瘤靶向损失{或获得}的基因区域;然后鉴定9q22.2-31.2区间内的实际新疾病基因和致病性疾病等位基因。因此，我们现在提出的具体步骤是：i）通过分别检查9q22.2-31.2区间的杂合性缺失（洛）{或增加的基因拷贝数}来分析该区间是否存在肿瘤抑制基因{或癌基因}，这些肿瘤发生在与该区域连锁的激酶中。然后通过确定这些家族性结肠肿瘤中共有的洛缺失（或增加的基因拷贝数）的最小区域，进一步缩小基因组间隔。ii）检查{5147个SNP多态性的综合组，平均间距为平均2.7kb，其捕获跨越9q22.2-31.2连锁区间的常见和罕见遗传变异;}之间的疾病关联，从而直接或间接地定位任何潜在的创始人疾病等位基因的位置，其将解释许多或所有这些结肠瘤形成家族中的肿瘤发展。iii）通过研究我们最好的连锁基因，直接寻找潜在的疾病基因和致病性疾病等位基因，通过对我们最大缩小的9q22.2-31.2间隔内的所有基因进行高通量测序，检查我们目前缩小的8.8Mb连锁间隔内包含的最多102个基因。iv）在我们的最佳连锁家族中构建“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。使用这些捕获的单倍体亲本染色体来测试我们最大限度缩小的间隔中的基因，以检测标准方法无法检测到的致病突变，包括外显子缺失测试和导致外显子跳跃的突变测试。该项目的成功将对公共卫生产生重大影响。公共卫生关系：结肠癌是美国癌症死亡的第二大原因，20%的结肠癌患者报告结肠癌家族史阳性，也影响父母或兄弟姐妹。确定一个新的基因是家族性结肠癌的常见原因，将允许识别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以挽救生命。