BRCA1 and BRCA2 Missense Variants of High and Low Clinical Significance Influence Lymphoblastoid Cell Line Post-Irradiation Gene Expression

The functional consequences of missense variants in disease genes are difficult to predict. We assessed if gene expression profiles could distinguish between BRCA1 or BRCA2 pathogenic truncating and missense mutation carriers and familial breast cancer cases whose disease was not attributable to BRCA1 or BRCA2 mutations (BRCAX cases). 72 cell lines from affected women in high-risk breast ovarian families were assayed after exposure to ionising irradiation, including 23 BRCA1 carriers, 22 BRCA2 carriers, and 27 BRCAX individuals. A subset of 10 BRCAX individuals carried rare BRCA1/2 sequence variants considered to be of low clinical significance (LCS). BRCA1 and BRCA2 mutation carriers had similar expression profiles, with some subclustering of missense mutation carriers. The majority of BRCAX individuals formed a distinct cluster, but BRCAX individuals with LCS variants had expression profiles similar to BRCA1/2 mutation carriers. Gaussian Process Classifier predicted BRCA1, BRCA2 and BRCAX status, with a maximum of 62% accuracy, and prediction accuracy decreased with inclusion of BRCAX samples carrying an LCS variant, and inclusion of pathogenic missense carriers. Similarly, prediction of mutation status with gene lists derived using Support Vector Machines was good for BRCAX samples without an LCS variant (82�C94%), poor for BRCAX with an LCS (40�C50%), and improved for pathogenic BRCA1/2 mutation carriers when the gene list used for prediction was appropriate to mutation effect being tested (71�C100%). This study indicates that mutation effect, and presence of rare variants possibly associated with a low risk of cancer, must be considered in the development of array-based assays of variant pathogenicity.疾病基因中错义变异（missense variant）的功能效应难以预测。本研究旨在探究基因表达谱能否区分BRCA1或BRCA2致病性截短突变与错义变异携带者，以及未携带BRCA1/2致病性突变的家族性乳腺癌患者（BRCAX病例）。本研究对72株来自高风险乳腺-卵巢家族受累女性的细胞系开展电离辐射处理后的表达谱检测，其中包含23名BRCA1突变携带者、22名BRCA2突变携带者与27名BRCAX个体。10名BRCAX个体携带被判定为低临床意义（Low Clinical Significance, LCS）的罕见BRCA1/2序列变异。BRCA1与BRCA2突变携带者的表达谱较为相似，其中错义突变携带者存在一定的亚聚类现象。多数BRCAX个体形成了独立的聚类，但携带LCS变异的BRCAX个体的表达谱与BRCA1/2突变携带者高度相似。高斯过程分类器（Gaussian Process Classifier）对BRCA1、BRCA2及BRCAX状态的预测最高准确率达62%，当纳入携带LCS变异的BRCAX样本与致病性错义突变携带者样本时，预测准确率会出现下降。类似地，采用支持向量机（Support Vector Machines）衍生的基因列表开展突变状态预测时，对于未携带LCS变异的BRCAX样本，预测效果优异（准确率82%~94%）；对于携带LCS变异的BRCAX样本，预测效果欠佳（准确率40%~50%）；而当预测所用基因列表与待检测的突变效应匹配时，致病性BRCA1/2突变携带者的预测准确率可提升至71%~100%。本研究表明，在开发基于芯片的变异致病性检测方法时，必须兼顾突变效应与可能关联低癌症风险的罕见变异的存在。