Benign breast disease (BBD) is a risk factor for breast cancer (BC); however, little is known about the genetic alterations present at the time of BBD diagnosis and how these relate to risk of incident BC. A subset of a long-term BBD cohort was selected to examine DNA variation across three BBD groups (42 future estrogen receptor-positive (ER+) BC, 36 future estrogen receptor-negative (ER−) BC, and 42 controls cancer-free for at least 16 years post-BBD). DNA extracted from archival formalin fixed, paraffin-embedded (FFPE) tissue blocks was analyzed for presence of DNA alterations using a targeted panel of 93 BC-associated genes. To address artifacts frequently observed in FFPE tissues (e.g., C>T changes), we applied three filtering strategies based on alternative allele frequencies and nucleotide substitution context. Gene-level associations were performed using two types of burden tests and adjusted for clinical and technical covariates. After filtering, the variant frequency of SNPs in our sample was highly consistent with population allele frequencies reported in 1 KG/ExAC (0.986, p < 1e−16). The top ten genes found to be nominally associated with later cancer status by four of 12 association methods(p < 0.05) were MED12, MSH2, BRIP1, PMS1, GATA3, MUC16, FAM175A, EXT2, MLH1 and TGFB1, although these were not statistically significant in permutation testing. However, all 10 gene-level associations had OR < 1 with lower mutation burden in controls compared to cases, which was marginally statistically significant in permutation testing (p = 0.04). Comparing between the three case groups, BBD ER+ cases were closer to controls in mutation profile, while BBD ER− cases were distinct. Notably, the variant burden was significantly higher in controls than in either ER+ or ER− cases. CD45 expression was associated with mutational burden (p < 0.001). Somatic mutations were more frequent in benign breast tissue from women who did not develop cancer, opening questions of clonal diversity or immune-mediated restraint on future cancer development. CD45 expression was positively associated with mutational burden, most strongly in controls. Further studies in both normal and premalignant tissues are needed to better understand the role of somatic gene mutations and their contribution to future cancer development.

中文翻译：

---

良性乳腺疾病组织中的体细胞突变与乳腺癌风险的关联

良性乳腺疾病 (BBD) 是乳腺癌 (BC) 的危险因素；然而，关于 BBD 诊断时存在的基因改变以及这些改变与 BC 事件风险的关系知之甚少。选择长期 BBD 队列的一个子集来检查三个 BBD 组（42 个未来雌激素受体阳性 (ER+) BC、36 个未来雌激素受体阴性 (ER-) BC 和 42 个无癌症对照组）的 DNA 变异。 BBD 后至少 16 年）。使用 93 个 BC 相关基因的靶向组分析从存档福尔马林固定、石蜡包埋 (FFPE) 组织块中提取的 DNA 是否存在 DNA 改变。为了解决在 FFPE 组织中经常观察到的伪影（例如，C>T 变化），我们应用了三种基于替代等位基因频率和核苷酸替代背景的过滤策略。使用两种类型的负担测试进行基因水平关联，并针对临床和技术协变量进行调整。过滤后，我们样本中 SNP 的变异频率与 1 KG/ExAC 中报告的群体等位基因频率高度一致（0.986，p < 1e-16）。通过 12 种关联方法中的四种（p < 0.05）发现名义上与晚期癌症状态相关的前 10 个基因是 MED12、MSH2、BRIP1、PMS1、GATA3、MUC16、FAM175A、EXT2、MLH1 和 TGFB1，尽管这些没有统计学意义在置换测试中具有重要意义。然而，与病例相比，所有 10 个基因水平关联的 OR < 1，对照组的突变负担较低，这在排列测试中具有轻微的统计学意义 (p = 0.04)。在三个病例组之间进行比较，BBD ER+ 病例的突变谱更接近对照组，而 BBD ER- 病例则不同。值得注意的是，对照组的变异负担明显高于 ER+ 或 ER- 病例。CD45 表达与突变负荷相关（p < 0.001）。体细胞突变在未患癌症的女性的良性乳腺组织中更为常见，这引发了克隆多样性或免疫介导对未来癌症发展的限制的问题。CD45 表达与突变负荷呈正相关，在对照组中最为强烈。需要对正常和癌前组织进行进一步研究，以更好地了解体细胞基因突变的作用及其对未来癌症发展的贡献。001)。体细胞突变在未患癌症的女性的良性乳腺组织中更为常见，这引发了克隆多样性或免疫介导对未来癌症发展的限制的问题。CD45 表达与突变负荷呈正相关，在对照组中最为强烈。需要对正常和癌前组织进行进一步研究，以更好地了解体细胞基因突变的作用及其对未来癌症发展的贡献。001)。体细胞突变在未患癌症的女性的良性乳腺组织中更为常见，这引发了克隆多样性或免疫介导对未来癌症发展的限制的问题。CD45 表达与突变负荷呈正相关，在对照组中最为强烈。需要对正常和癌前组织进行进一步研究，以更好地了解体细胞基因突变的作用及其对未来癌症发展的贡献。