CNV Identification: Prostate Cancer (PCa) vs Benign Prostatic Hyperplasia (BPH) Human DNA Samples. Homo sapiens

Copy number variations (CNVs) in the human genome have been linked to various carcinomas including prostate cancer (PCa). This study was conducted to identify CNVs in high grade PCa. We performed a pilot genome-wide CNV analysis in 36 subjects (18 high grade PCa and 18 benign prostatic hyperplasia) using array comparative genomic hybridization (aCGH) technique. Array results were validated using PCR-based copy number counting method. A total of 339 CNV regions were found to be unique to PCa subjects in this cohort (P < 0.05). Data segregation and filtering revealed six putative CNV loci associated with susceptibility to PCa. Of these, four were rare (1q21.3, 15q15, 3q27.2 and 7p12.1) and one was a novel copy number gain (12q23.1), harbouring genes such as the ARNT, THBS1, SLC5A8 and DDC which are crucial in the p53 and cancer pathways. Another CNV was a loss at 8p11.21 which contains the SFRP1 gene from the Wnt signalling pathway, known for its interaction with androgen receptors as reported for urological malignancy. Cross comparison analysis with genes already known to be associated with PCa revealed significant CNVs involved in crucial biological processes that elicit cancer pathogenesis via cytokine production, disease progression through endothelial cell proliferation and xenobiotic metabolism. In conclusion, these findings suggest that the CNV regions identified could provide an insight into the development of high grade PCa. Overall design: 36 samples were analysed for the purpose of CNV identification (discovery cohort) and 46 other samples ( a different subset of samples) were included in the validation cohort. For the discovery cohort, 18 PCa and 18 BPH samples were used as case and control respectively. Controls in this study was used as the reference itself in order to avoid misinterpretation of data due to reference sample of a different genetic makeup i.e. Yoruba Male- provided in the kit.人类基因组中的拷贝数变异（Copy number variations, CNVs）已被证实与包括前列腺癌（prostate cancer, PCa）在内的多种恶性肿瘤相关。本研究旨在鉴定高级别前列腺癌中的拷贝数变异。我们采用阵列比较基因组杂交（array comparative genomic hybridization, aCGH）技术，对36名受试者（18名高级别前列腺癌患者与18名良性前列腺增生（benign prostatic hyperplasia, BPH）患者）开展先导性全基因组拷贝数变异分析。阵列检测结果采用基于聚合酶链式反应（polymerase chain reaction, PCR）的拷贝数计数方法进行验证。本队列中共计发现339个前列腺癌患者特异性拷贝数变异区域（P < 0.05）。经过数据分离与过滤，共筛选出6个与前列腺癌易感性相关的潜在拷贝数变异位点。其中4个为罕见变异（1q21.3、15q15、3q27.2及7p12.1），1个为全新的拷贝数扩增区域（12q23.1），该区域携带有ARNT、THBS1、SLC5A8及DDC等基因，这些基因在p53通路与癌症通路中发挥关键作用。另有一个拷贝数缺失变异位于8p11.21，该区域包含Wnt信号通路中的SFRP1基因，已有研究表明该基因与泌尿生殖系统恶性肿瘤中的雄激素受体存在相互作用。与已报道的前列腺癌相关基因进行交叉比对分析后发现，这些显著的拷贝数变异参与了诸多关键生物学过程：包括通过细胞因子产生诱发癌症致病过程、通过内皮细胞增殖促进疾病进展，以及参与外源性物质代谢。综上，本研究鉴定出的拷贝数变异区域可为高级别前列腺癌的发生发展提供新的见解。实验整体设计：本研究共纳入两类分析队列：其一为发现队列，共计36份样本（18份前列腺癌样本与18份良性前列腺增生样本，分别作为病例组与对照组），用于拷贝数变异的筛选鉴定；其二为验证队列，包含46份独立的样本子集。为避免因使用试剂盒自带的不同遗传背景参考样本（即约鲁巴男性样本）而导致的数据解读偏差，本研究以研究自身的对照组样本作为参考。