Identification of Melanoma Susceptibility Gene at 1p22

1p22 黑色素瘤易感基因的鉴定

• 批准号: 6944197
• 负责人: JEFFREY M. TRENT
• 金额: $ 56.2万
• 依托单位: TRANSLATIONAL GENOMICS RESEARCH INST
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-27 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6944197
• 关键词: alleles; bioinformatics; cancer risk; cell line; clinical research; comparative genomic hybridization; experimental designs; family genetics; gene expression; gene mutation; genetic screening; genetic susceptibility; genotype; high throughput technology; human subject; lymphocyte; melanocyte; melanoma; microarray technology; neoplasm /cancer genetics; nucleic acid sequence; single nucleotide polymorphism

DESCRIPTION (provided by applicant): Despite decades of research, metastatic cutaneous malignant melanoma (CMM) remains an incurable disease, demonstrating a median survival time of 9 months, with a 5-year survival rate of less than 5 percent. Further, over the past 20 years, the incidence of CMM has increased dramatically worldwide. Critical to this study, a positive family history of the disease is among the most established risk factors for CMM; 10% of CMM cases result from an inherited predisposition. Although mutations in two genes, CDKN2A and CDK4, confer an increased risk of CMM, they account for only 20% - 25% of families with multiple cases of CMM. We hypothesize that that there are additional CMM-predisposition genes, and this application provides an empirically based, technologically innovative approach to identify one such gene. We have performed a genome-wide linkage scan of 82 CMM kindreds with no involvement of CDKN2A or CDK4, and have identified a novel CMM susceptibility locus on chromosome 1 (1p22). To identify the melanoma susceptibility gene at this locus (Aim 1), we are integrating multiple experimental methods aimed at prioritizing candidate genes for mutation screening. Specifically, we will: (a) perform high-resolution SNP-typing and look for evidence of haplotype sharing between CMM families in order to further narrow the critical region; (b) design a custom oligonucleotide microarray representing all potential coding sequences within the 1p22 critical region in order to identify novel genes and to characterize tissue-specific gene expression for the purpose of candidate gene prioritization; and (c) design a custom 1p22 oligonucleotide microarray for comparative genomic hybridization (CGH) and look for partial- or whole-gene deletions in DNA from patient lymphocytes as well as melanoma cell lines with hemizygous loss at 1p22. Based on these data, we will prioritize our gene candidates and (d) screen genes for mutations using DNA sequencing. Following the identification of the 1p22 melanoma susceptibility gene, we will determine the prevalence of 1p22 gene mutation/loss (Aim 2) in a panel of melanoma cell lines, tumors, and nevi, and propose an experimental approach to understand its mechanism of action. Lastly, we will test the hypothesis that Iow-penetrance susceptibility alleles of the melanocortin receptor (MCIR) modify the penetrance of 1p22 susceptibility gene mutations (Aim 3) and genotype both affected and unaffected members of our 1p22-mutation positive families for these alleles.

描述（由申请人提供）：尽管经过数十年的研究，转移性皮肤恶性黑色素瘤（CMM）仍然是一种无法治愈的疾病，中位生存时间为 9 个月，5 年生存率低于 5%。 此外，在过去 20 年中，CMM 的发病率在全球范围内急剧增加。 对本研究至关重要的是，该疾病的阳性家族史是 CMM 最明确的危险因素之一。 10% 的 CMM 病例是由遗传倾向引起的。 尽管 CDKN2A 和 CDK4 这两个基因的突变会增加 CMM 的风险，但它们仅占多发 CMM 病例家庭的 20% - 25%。 我们假设存在额外的 CMM 易感基因，并且该应用提供了一种基于经验的技术创新方法来识别此类基因。 我们对 82 个不涉及 CDKN2A 或 CDK4 的 CMM 家族进行了全基因组连锁扫描，并在 1 号染色体 (1p22) 上鉴定了一个新的 CMM 易感位点。 为了确定该位点的黑色素瘤易感基因（目标 1），我们正在整合多种实验方法，旨在优先考虑突变筛选的候选基因。 具体来说，我们将： (a) 进行高分辨率 SNP 分型并寻找 CMM 家族之间单倍型共享的证据，以进一步缩小关键区域； (b) 设计代表 1p22 关键区域内所有潜在编码序列的定制寡核苷酸微阵列，以便识别新基因并表征组织特异性基因表达，从而确定候选基因的优先顺序； (c) 设计用于比较基因组杂交 (CGH) 的定制 1p22 寡核苷酸微阵列，并寻找患者淋巴细胞以及 1p22 半合子缺失的黑色素瘤细胞系 DNA 中的部分或全基因缺失。 根据这些数据，我们将优先考虑候选基因，并 (d) 使用 DNA 测序筛选基因是否存在突变。 在鉴定出 1p22 黑色素瘤易感基因后，我们将确定一组黑色素瘤细胞系、肿瘤和痣中 1p22 基因突变/丢失（目标 2）的患病率，并提出一种实验方法来了解其作用机制。 最后，我们将检验以下假设：黑皮质素受体 (MCIR) 的低外显率易感性等位基因会改变 1p22 易感性基因突变的外显率（目标 3），并对这些等位基因的 1p22 突变阳性家族中受影响和未受影响的成员进行基因分型。