wes文献抄读2
Title：Clinical implication of tumor mutational burden in patients with HER2-positive refractory metastaticbreast cancer
Journal：OncoImmunology
IF:5.503
Personal Comment：
1这篇文章的思路来源：既往报道TMB与肿瘤的免疫治疗有关系，是否与化疗联合靶向治疗有关
2.推理：TMB是肿瘤的SNV，非同义突变，导致表面蛋白变化，出现新的抗原，激活患者体内免疫，而HER-2靶向治疗药物，有免疫性质，免疫协同作用，那么，TMB是否能预测HER-2靶向治疗的疗效，提出假说。
3.文章定义两个概念，100以上体细胞SNV（单核苷酸变异）非同义突变（定义为高TMB），clinical benefit定义： (PFS > 12 months and OS > 2 years)
4.文章提出了一个争议问题，TMB高低组定义，，TMB对预后的作用（TCGA一个报道是预后差）
5.文章结论，如果这个假说通过大规模数据证实，那么我们可以通过wes测序找到高TMB的HER-2阳性MBC人群，这组人群如果一线治疗失败（标准化疗联合HER-2靶向治疗），可能再二线靶向治疗（挽救性治疗）获益。有更好的os。
tumor mutational burden TMB：肿瘤突变负荷
人群：确诊的HER-2阳性复发转移性乳腺癌
方法：全外显子测序
样本：FFPE tumor samples and matched normal tissue.
患者：共46人，13人ER阳性，9人PR阳性，26人MBC中20人复发
16人存在100以上体细胞SNV（单核苷酸变异）非同义突变（定义为高TMB）
中位OS:高TMB组 85.8个月，低TMB组44.9个月
结论：高TMB是好的生存的预测标记，对于经过传统HER靶向治疗和化疗的患者。
憧憬：找到一个人群，在HER-2靶向治疗后复发但是对免疫治疗有良好反应的人群。
背景：HER-2阳性率15-20%，
提出临床问题，对HER-2治疗的原发和再发耐药
目前临床治疗背景：曲妥珠单抗联合化疗中位进展时间7.4个月，客观反映率50%，
技术方法背景：WES揭示了临床结果和TMB之间的关系--参考文献8，9
TMB定义： TMB被定义为过滤后，体细胞非同义单核苷酸变体的总和（SNV）。
提出假说：We hypothesized that TMB is a potential prognostic or predictivemarker candidate for conventional treatments, includingHER2-targeting agents in HER2-positive MBC
假说依据：several WES studies have demonstrateda significant correlation between median frequency ofsomatic mutations per megabase and median response rate to immunotherapy across solid tumors.Studies have also suggested that the antigenicity of tumor cells is highly correlated with response to immune checkpoint inhibitors
二线化疗方案：环磷酰胺+阿霉素
TMB分组的生存分析
HER-2靶向治疗药物：trastuzumab， pertuzumab ， lapatinib.
mPFS 低TMB VS 高TMB(9.6 months vs 17.1 months) p = 0.285 一线化疗人群
mPFS 低TMB VS 高TMB(4.4 months vs 5.6 months) p = 0.527 二线化疗人群
Pearson’s linear correlation analysis according to TMB status：对临床获益人群和非获益人群做比较，Significantly greater clinical benefits were observed in thehigh TMB group compared with the low TMB group (p=0.046)
clinical benefit定义： (PFS > 12 months and OS > 2 years)
FoundationOne®是国内首个针对实体肿瘤患者的全面基因组测序分析服务（Comprehensive Genomic Profiling，简称CGP）。患者只需通过一次检测，即可得到FoundationOne®呈现的全面基因组图谱分析报告。这一报告将为临床医生的治疗决策提供患者的全面分子信息，发现更多的治疗选择，帮助制定更有针对性的临床治疗方案。
When the FoundationOne was classified as high molecular abnormality(>= 20 mutations/Mb), the overall survival was significantly difference.
mOS at low and high number of molecular alteration, 60.0 months vs.104.3 months, (p=0.017)
mPFSby low and high number of molecular alteration ,13.3 months vs. 22.1 months,
(p = 0.160)
there was no significant difference in overall survival when classified as intermediate molecular abnormality (>= 6 mutations/Mb).
讨论：This study demonstrated that high TMB may be a good prognostic marker in HER2-positive MBC patients who have received standard treatments. The mOS was significantly longer in the high TMB status group based on WES.
We also hypothesized that a neoantigen might affect the clinical benefits of a HER2-targeting agent and cytotoxic chemotherapy.
背景：体细胞非同义SNV的总和是由于新抗原增加，对化疗的反应良好的预测因子。
The neoantigen causes non-synonymous SNVs that alter amino acid coding sequences
Some mutated peptides present on tumor cell surface and are recognized by neoantigen-specific T cells, isolated from tumor-infiltrating lymphocytes (TILs)
Defining high TMB in each tumor type is still controversial.
In this study, high TMB was predefined as >100 nonsynonymous SNVs based on results showing that melanoma patients who receive clinical benefits from ipilimumab were
classified as high neoantigen with mutational loads >100.
争议：TCGA data, the authors defined high TML as median mutation load >65 mutations
and reported no differences in prognosis in an ER-negative sub-group, while the HER2-positive sub-group was not analyzed.
In addition, it has been reported that patients with high mutation load in ER-positive breast cancers demonstrate poor prognosis.
tumor burden mutation analysis and chi-square test were performed to demonstrate
clinical benefits in the high TMB group.为什么用卡方检验？？这个我回去看一下卡方检验，然后再写出来，学习统计原理
文章限制：单中心小样本可能存在选择偏倚，并提出解决方法。
然后提出课题优势：晚期转移性乳腺癌，HER-2阳性靶向治疗后复发人群。
提出假说：we hypothesized that HER2-positive breast cancer patients with a high mutational
burden and a poor response to cytotoxic chemotherapy would have good clinical outcomes with immunotherapy.
据我们所知，这是第一份HER2阳性乳腺癌中的TMB显示出对HER2联合的标准化疗反应
相关的报道。
In conclusion, high TMB was the only independent prognostic factor for good mOS
QIAamp DNA FFPE Tissue kit试剂盒可以提取FFPE样本的DNA
比对：BWA-MEM
比对工具：GATK
MuTect software：call SNV（TCGA采取的四款软件：MuSE,varscan，MuTect，SomaticSniper）
绘图工具：GraphPad Prism 7