A new approach to identify rare genetic variants influencing melanoma risk

描述（由申请人提供）：许多全基因组关联研究（GWAS）已成功地将常见SNP与复杂性状的病因学联系起来。目前发现的大多数变异都使风险增加相对较小（1.1-1.5倍），仅能解释一小部分家族聚集性。最近的研究表明，常见疾病可能是由于具有广泛等位基因频率的功能障碍性变体。到目前为止，罕见变异研究仅限于少数表型和基因，但测序技术的进步应该会导致候选基因和基因组的广泛关联研究。如果罕见的变异比常见的变异有更大的影响，这应该有助于它们的检测。此外，它们的识别应该对风险评估、疾病预防和治疗产生更大的影响。然而，罕见变异的分析是具有挑战性的，因为用于常见变异的方法动力不足。以前，我们使用的数据，从突变筛查乳腺癌患者和对照组证明有能力检测证据的致病性从截短和剪接连接变异和罕见的错义取代。该方法涉及将病例和/或对照中观察到的罕见错义置换分层为从最不可能到最可能进化上有害的一系列等级，然后进行逻辑回归趋势检验以比较病例与对照中变体等级的频率分布。最初的模型是为了评估乳腺癌相关基因中错义替换的致病性而开发的。在这里，我们建议测试我们的分析策略的效率，皮肤恶性黑色素瘤（CMM）。为了识别新的风险等位基因，我们将在EPIC队列中招募的10个欧洲国家的1，300多例病例和1，300例匹配对照中筛选色素沉着途径的最强候选基因。CMM提供了一个独特的模型，研究基因-基因和基因-环境相互作用的多因素疾病的发展，因为主要的环境因素（暴露于太阳紫外线辐射）和已知的易感基因之间的关系是合理的理解。CDKN 2A和CDK 4的高风险突变由约20-25%的黑色素瘤易感家族携带。相反，色素沉着基因MC 1 R中的一些错义替换已被证明是中度风险或中度风险的易感等位基因，并且也增加了CDKN 2A突变的发生率。最后，两个最近的GWAS在MC 1 R或相同途径的基因中鉴定出低多态性SNP。相关的SNP将占家族相对风险的不超过12%。因此，大多数的遗传易感性CMM仍然有待解释。在强有力的候选人验证我们的方法后，设想对整个生化途径的基因进行大规模并行测序，以生成涉及黑色素瘤易感性的致病序列变体的风险频谱的全面图片。 公共卫生相关性：恶性黑色素瘤是一种罕见的黑色素细胞肿瘤，由于其侵袭性，导致大多数与皮肤癌相关的死亡。自世纪中期以来，黑色素瘤已成为世界范围内白皮肤人群的重要健康问题，因为其发病率比任何其他类型的恶性肿瘤上升得更快。本研究的目的是确定新的黑色素瘤易感基因和与黑色素瘤风险增加相关的致病序列变异的特征。识别易感个体可能有助于增加防晒和在疾病的癌前阶段早期发现黑色素细胞肿瘤，改变对阳光和晒黑的态度，并保护皮肤免受紫外线损伤。

DESCRIPTION (provided by applicant): A number of genome-wide association studies (GWAS) have successfully implicated common SNPs in the etiology of complex traits. Most variants identified so far confer relatively small increments in risk (1.1-1.5-fold), and explain oly a small proportion of familial clustering. Recent studies have demonstrated that common diseases can be due to dysfunctional variants with a wide spectrum of allele frequencies. So far, rare variants studies have been limited to a handful of phenotypes and genes, but the advancement of sequencing technologies should lead to widespread association studies of candidate genes and genomes. If rare variants have larger effects than common variants, this should aid in their detection. Also their identification should have a greater impact on risk assessment, disease prevention and treatment. However, the analysis of rare variants is challenging since methods used for common variants are underpowered. Previously, we used data from mutation screening of breast cancer patients and controls to demonstrate the ability to detect evidence of pathogenicity from both truncating and splice junction variants and rare missense substitutions. The method involves stratifying rare missense substitutions observed in cases and/or in controls into a series of grades ordered from least to most likely to be evolutionarily deleterious, followed by a logistic regression trend test to compare the frequency distributions of the grades of variants in cases versus controls. The original model was developed to assess the pathogenicity of missense substitutions in breast cancer-related genes. Here we propose to test the efficiency of our analysis strategy to cutaneous malignant melanoma (CMM). To identify novel risk alleles, we will mutation screen the strongest candidate genes of the pigmentation pathway in over 1,300 cases and 1,300 matched controls from 10 European countries enrolled in the EPIC cohort. CMM provides a unique model for studies of gene-gene and gene-environmental interactions in the development of multifactorial diseases, since relationships between the major environmental factor (exposure to solar UV radiation) and known susceptibility genes are reasonably well understood. High-risk mutations in CDKN2A and CDK4 are carried by about 20-25% of melanoma-prone families. In contrast, some missense substitutions in the pigmentation gene MC1R have been proven to be modest-risk or intermediate-risk susceptibility alleles, and also to increase the penetrance of CDKN2A mutations. Finally, two recent GWAS identified low- penetrance SNPs in MC1R or in genes of the same pathway. Associated SNPs will account for no more than 12% of the Familial Relative Risk. Thus, the majority of the genetic susceptibility to CMM remains to be explained. After validation of our method on strong candidates, massive parallel sequencing of genes of entire biochemical pathways is envisaged to generate a comprehensive picture of the risk-frequency spectrum for pathogenic sequence variants involved in susceptibility to melanoma. PUBLIC HEALTH RELEVANCE: Malignant melanoma is a rare tumor of melanocytes that, because of its aggressive nature, causes the majority of deaths related to skin cancer. Since the mid-20th century, melanoma has become an important health problem in fair-skinned populations worldwide, since its incidence has climbed faster than any other type of malignancy. The goal of this study is the identification of new melanoma susceptibility genes and the characterization of the pathogenic sequence variants associated with increased risk of developing melanoma. Identification of susceptible individuals may aid in increasing sun protection and early detection of melanocytic tumors at the precancerous stage of the disease, altering attitudes toward sunlight and suntans, and protecting the skin from UV damage in populations at risk.