Objective: To explore the relationship between germline rare variants of bromodomain and extraterminal domain (BET) protein family-encoding genes and susceptibility to cancer in some regions of China. Methods: Capturing probes were designed for bromodomain-containing protein 2 (BRD2), BRD3 and BRD4 genes, and Illumina high-throughput sequencing platform was used to conduct targeted sequencing of genomic DNA of peripheral blood leukocytes from 1 673 patients with cancer and 1 661 individuals without cancer recruited between October 2015 and July 2018 from Chinese PLA General Hospital, the Second Affiliated Hospital of Guangxi Medical University, People's Hospital of Macheng City, Hubei Province and Geneplus-Beijing Co. Ltd. Mutation detection and analysis were carried out according to the genome analysis toolkit (GATK) best practice guidelines, ANNOVAR and VEP software were used for annotation, and germline rare variants in BET family were screened. To determine potential pathogenic germline rare variants, clinical and experimental evidence was obtained from the ClinVar database and SIFT and Polyphen-2 softwares were used to predict pathogenicity. Fisher's exact test was used to compare the difference of the carrying rate of variants in the case group and the control group, and multivariate regression analysis was performed with the SKAT software with sex and age used as covariates. Results: Among the 1 673 cancer patients, 911 were males and 762 were females, with the mean age was (57.9±11.7) years. There were 1, 111 cases (66.4%) of lung cancer, 266 cases (15.9%) of colorectal cancer, 186 cases of breast cancer (11.1%), and 110 cases (6.6%) of esophagus or gastric cancer. In the same period 1, 661 non-tumor control individuals were recruited, including 821 males and 840 females, with the mean age was (44.5±13.9) years. It was observed that there were 4 potential pathogenic germline rare variants in BRD2 gene carried by 17 patients with cancer, 5 potential pathogenic germline rare variants in BRD3 gene and 8 potential pathogenic germline rare variants in BRD4 gene. The carrying rate of potential pathogenic germline rare variants in BRD2 gene in cancer patients was 1.02% (17/1 673), significantly higher than that in controls without cancer [0 (0/1 661); OR=+∞, 95%CI: 4.81-+∞, P<0.001]. The carrying rate of potential pathogenic germline rare variants in BRD3 gene in cancer patients was 0.24% (4/1 673), and the difference was not statistically significant compared with controls without cancer [0.12% (2/1 661); OR=1.99, 95%CI: 0.46-10.47, P=0.690]. The carrying rate of potential pathogenic germline rare variants in BRD4 gene in cancer patients was 0.18% (3/1 673), and the difference was not statistically significant compared with controls without cancer [0.36% (6/1 661); OR=0.50, 95%CI: 0.14-2.08, P=0.340]. Furthermore, the dataset of whole exome sequencing of Chinese individuals in "Huabiao Project" was used as an additional control, and the rate of carrying BRD2 rare variants in cancer patients was 17/3 346 (0.51%), significantly higher than that in controls without cancer [0.07% (3/4 154); OR=7.07, 95%CI: 2.32-22.83, P<0.001]. Among the 17 patients carrying 4 potentially pathogenic germline rare variants of BRD2 gene, 9 were patients with lung cancer, 6 were patients with colorectal cancer, 1 was patient with breast cancer, and 1 was patients with esophagus or gastric cancer. The carrying rate of potential pathogenic germline rare variants in BRD2 gene in lung cancer patients was 0.81 (9/1 111), significantly higher than that in controls without cancer [0(0/1 661); OR=+∞, 95%CI: 3.95-+∞,P<0.001]. The carrying rate of potential pathogenic germline rare variants in BRD2 gene in patients with colorectal cancer was 2.26% (6/266), significantly higher than that in controls without cancer [0(0/1 661); OR=+∞, 95%CI: 9.03-+∞, P<0.001]. Wilcoxon rank-sum test results showed that patients with colorectal cancer carrying BRD2 rare variants had an earlier age at diagnosis [(47.0±7.4) vs (57.2±12.1) years old, P=0.017]. Conclusions: BRD2 gene may be served as a candidate genetic susceptibility gene for lung cancer and colorectal cancer. Carrying BRD2 potential pathogenic germline rare variants is associated with higher risk of lung cancer and colorectal cancer, and with earlier age of colorectal cancer.
目的： 探讨溴结构域和超末端结构域蛋白（BET）家族编码基因胚系罕见变异与中国部分地区人群恶性肿瘤易感性的关系。 方法： 针对溴结构域蛋白2（BRD2）、BRD3、BRD4基因设计捕获探针，利用Illumina高通量测序平台，对2015年10月至2018年7月解放军总医院、广西医科大学第二附属医院、湖北省麻城市人民医院以及北京吉因加科技有限公司募集的1 673例恶性肿瘤患者和1 661例非肿瘤对照者的外周血白细胞基因组DNA进行靶向测序。根据基因组分析工具包（GATK）最佳实践指南进行变异检测分析，采用ANNOVAR、VEP软件进行注释，筛选BET家族中胚系罕见变异。为了确定潜在致病性胚系罕见变异，在ClinVar数据库中检索其致病性的临床和实验证据，并采用SIFT和PolyPhen-2软件预测变异的致病性。以Fisher′s 精确检验比较病例组和对照组变异率的差异，采用SKAT软件将性别、年龄作为协变量进行多因素回归分析。 结果： 1 673例肿瘤患者中，男911例，女762例；年龄（57.9±11.7）岁；肺癌1 111例（66.4%），肠癌266例（15.9%），乳腺癌186例（11.1%），食管癌或胃癌110例（6.6%），同期招募非肿瘤对照1 661例，其中男821例，女840例；年龄（44.5±13.9）岁。BRD2基因中共有4个潜在致病性胚系罕见变异，且这4个变异仅存在于17例肿瘤患者中。从肿瘤患者和非肿瘤对照中共筛选出5个存在于BRD3基因上的潜在致病性胚系罕见变异，以及8个存在于BRD4基因上的潜在致病性胚系罕见变异。BRD2基因在肿瘤患者中的潜在致病性胚系罕见变异率为1.02%（17/1 673），高于非肿瘤对照［0（0/1 661）；OR=+∞，95%CI：4.81~+∞，P<0.001］。BRD3基因在肿瘤患者中的潜在致病性胚系罕见变异率为0.24%（4/1 673），与非肿瘤对照相比，差异无统计学意义［0.12%（2/1 661）；OR=1.99，95%CI：0.46~10.47，P=0.690］。BRD4基因在肿瘤患者中的潜在致病性胚系罕见变异率为0.18%（3/1 673），与非肿瘤对照相比，差异无统计学意义［0.36%（6/1 661）；OR=0.50，95%CI：0.14~2.08，P=0.340］。进一步将“华表计划”中国人群全外显子测序数据集用作对照，BRD2基因在肿瘤患者中的变异率为17/3 346（0.51%），明显高于对照［0.07%（3/4 154）；OR=7.07，95%CI：2.32~22.83，P<0.001］。17例携带BRD2基因4个潜在致病性胚系罕见变异患者中，肺癌9例，肠癌6例，乳腺癌1例，食管癌或胃癌1例。BRD2基因在肺癌患者中的潜在致病性胚系罕见变异率为0.81（9/1 111），高于非肿瘤对照［0（0/1 661）；OR=+∞，95%CI：3.95~+∞，P<0.001］；BRD2基因在肠癌患者中的潜在致病性胚系罕见变异率为2.26%（6/266），明显高于非肿瘤对照［0（0/1 661）；OR=+∞，95%CI：9.03~+∞，P<0.001］。携带BRD2基因罕见变异的患者具有更早的肠癌发病年龄［（47.0±7.4）比（57.2±12.1）岁，P=0.017］。 结论： BRD2基因可能是肺癌、肠癌的候选遗传易感基因，携带BRD2基因潜在致病性胚系罕见变异具有更高的肺癌、肠癌发病风险以及更早的肠癌发病年龄。.