Additional file 2 of Molecular characteristics of breast tumors in patients screened for germline predisposition from a population-based observational study

Additional file 2: Supplementary tables. Table S1. Clinicopathological characteristics of patients and tumors in SCAN-B divided by screening subpopulation and relevant clinical subgroups/PAM50 molecular subtypes. Table S2. Genes included in the original two signatures and whether they were used for calculating the in silico rank scores in our work. Table S3. Differentially expressed genes between screening subpopulations by clinical subgroups and PAM50 molecular subtypes. Table S4. Significant pathways overrepresented in up- and downregulated genes found in screened TNBC patients compared to non-screened. Table S5. Estimated cell fraction and enrichment score mean and standard deviation divided by clinical subgroups and PAM50 molecular subtypes. Table S6. Top 10 genes with most expressed somatic variants per clinical subgroup and their distribution in patients with regards to screening status and presence of somatic variants. Table S7. List of PGVs and VUS identified in 900 SCAN-B patients screened for germline variants. Table S8. Clinicopathological characteristics of patients with and without PGVs. Table S9. Differentially expressed genes between patients with and without PGVs divided by clinical subgroups and PAM50 molecular subtypes. Table S10. Significant pathways overrepresented in up- and downregulated genes found in ER+/HER2− patients with PGVs when compared to those without variants. Table S11. Estimated cell fraction and enrichment score mean and standard deviation by PGV status of patients divided by clinical subgroups and PAM50 molecular subtypes. Table S12. Top 10 genes with most expressed somatic variants within patients tested for germline variants in three specific genes and their distribution in patients with regards to presence of somatic variants and PGVs. Table S13. All SCAN-B patients used in this study, screening status, for which of the 11 genes analyzed a patient was tested, and whether any PGV was found.

附加文件2：补充表格。
表S1：SCAN-B队列中按筛查亚群、相关临床亚组及PAM50分子亚型划分的患者与肿瘤临床病理特征。
表S2：纳入原始两个基因特征的基因，以及本研究中是否将其用于计算虚拟排名评分（in silico rank scores）。
表S3：按临床亚组及PAM50分子亚型划分的筛查亚群间的差异表达基因。
表S4：与未筛查的三阴性乳腺癌（Triple-Negative Breast Cancer, TNBC）患者相比，筛查的TNBC患者中上调及下调基因所富集的显著通路。
表S5：按临床亚组及PAM50分子亚型划分的估计细胞分数及富集评分的均值与标准差。
表S6：每个临床亚组中体细胞变异表达量最高的前10个基因，以及这些基因在患者中按筛查状态与体细胞变异存在情况划分的分布特征。
表S7：在900例接受生殖系变异筛查的SCAN-B患者中鉴定出的致病性生殖系变异（Pathogenic Germline Variant, PGV）与意义未明变异（Variant of Uncertain Significance, VUS）列表。
表S8：携带与未携带PGV的患者临床病理特征。
表S9：按临床亚组及PAM50分子亚型划分的携带与未携带PGV的患者间的差异表达基因。
表S10：与未携带变异的雌激素受体阳性（Estrogen Receptor-positive, ER+）/人表皮生长因子受体2阴性（Human Epidermal Growth Factor Receptor 2-negative, HER2-）患者相比，携带PGV的该类患者中上调及下调基因所富集的显著通路。
表S11：按临床亚组及PAM50分子亚型划分、按患者PGV状态分层的估计细胞分数及富集评分的均值与标准差。
表S12：在针对3个特定基因开展生殖系变异检测的患者中，体细胞变异表达量最高的前10个基因，以及这些基因在患者中按体细胞变异存在情况与PGV携带状态划分的分布特征。
表S13：本研究纳入的所有SCAN-B患者信息、筛查状态、患者接受检测的11个分析基因清单，以及是否检出PGV。