Unraveling metastatic progression of breast cancer

To reconstruct the trajectories of BC progression, we performed exome sequencing (Illumina HiSeq2000, Truseq DNA sample preparation kit v2 and Exome Enrichment Kit v2; alignement done with BWA, substitutions and indels called with GATK and DINDEL respectively) coupled to validation by Sequenom and deep re-sequencing (ongoing), as well as copy number (CN) analyses (Oncoscan, Affymetrix) on DNA from matched primary (n=1-6/pt), axillary lymph node (ALN, n=1-6 for 4 pts), local recurrence (for 1 pt) and distant metastatic (n=1-5/pt) FFPE samples obtained from an autopsy series of 10 BC pts.EGA study EGAS00001000760

为重建乳腺癌（Breast Cancer, BC）的进展轨迹，本研究对匹配的福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）样本开展了外显子组测序：采用Illumina HiSeq2000测序平台，搭配Truseq DNA样本制备试剂盒v2与外显子组捕获试剂盒v2；序列比对通过BWA完成，单碱基替换与插入缺失分别由GATK与DINDEL进行检测。同时辅以Sequenom平台验证与深度重测序（研究正在进行中），并利用Affymetrix Oncoscan芯片完成拷贝数（CopyNumber, CopyNumber, CN）分析。本研究纳入10例乳腺癌患者的尸检队列，所获样本包括原发灶样本（每例患者1~6份，n=1~6/pt）、腋窝淋巴结（Axillary Lymph Node, ALN）样本（4例患者各1~6份）、1例患者的局部复发灶样本，以及远处转移灶样本（每例患者1~5份，n=1~5/pt）。本研究对应的欧洲基因组学档案（European Genome-phenome Archive, EGA）研究项目编号为EGAS00001000760。