Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

在德克萨斯大学MD安德森癌症中心开展的一项生物标志物发现研究中，我们前瞻性收集了37例未接受任何全身治疗的乳腺癌患者的配对细针抽吸活检（Fine-Needle Aspiration, FNA）与核心针活检（Core Needle Biopsy, CBX）样本。我们在核心活检组织中鉴定出293个过表达探针组，其中包含5个高度共表达的基因簇（元基因，metagenes），分别对应免疫功能通路与细胞外基质成分。为筛选肿瘤基质相关基因，我们对比了37例乳腺癌患者的细针（基质贫乏型）与核心针（基质丰富型）活检配对样本的基因表达谱。本研究获取了原发肿瘤术前配对匹配的细针抽吸活检与核心针活检样本，按照厂商标准操作流程完成RNA提取，并将其杂交至Affymetrix微阵列。