Examination of gene fusion status in archival samples of alveolar rhabdomyosarcoma entered on the intergroup rhabdomyosarcoma study-III trial - A report from the Children's Oncology Group
Examination of gene fusion status in archival samples of alveolar rhabdomyosarcoma entered on the intergroup rhabdomyosarcoma study-III trial - A report from the Children's Oncology Group
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DOI：
10.2353/jmoldx.2006.050124
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发表时间：
2006-05-01
影响因子：
4.1
通讯作者：
Breitfeld, PP
中科院分区：
文献类型：
--
作者：
Barr, FG;Smith, LM;Breitfeld, PP
腺泡状横纹肌肉瘤 (ARMS) 是一种软组织癌，其中染色体易位；生成 PAX3-FKHR 和 PAX7-FKHR 基因融合体。为了改进档案样本中融合检测的方法，我们开发了一种针对这些融合转录本的实时逆转录酶-聚合酶链反应测定法。通过合并共有引物和基因特异性探针，在一项测定中确定了融合体的存在和亚型。我们将这种方法应用于来自组间横纹肌肉瘤研究 (IRS)-III 临床试验的 78 个福尔马林固定、石蜡包埋的 ARMS 肿瘤的方便样本，并在 59 个病例 (76%) 中获得了满意的结果。融合类型的分布为 35 种 (59%) PAX3-FKHR、11 种 (19%) PAX7-FKHR 和 13 种融合阴性 (22%)。在随后的临床分析中，我们发现与无法进行融合分析的 IRS-III ARMS 病例相比，分析融合状态的 IRS-III ARMS 病例的结果显着改善。这一结果的基础无法用已知的预后临床因素来解释，多变量分析证实我们的方便样本不能代表整个 IRS-III 队列。总之，尽管这些稳健的测定为档案材料的相关研究提供了新的机会，但我们的第一个应用说明了使用便利样本进行分子临床相关研究的重要局限性。
Alveolar rhabdomyosarcoma (ARMS) is a soft tissue cancer in which chromosomal translocations; generate PAX3-FKHR and PAX7-FKHR gene fusions. To improve the approach for fusion detection in archival samples, we developed a real-time reverse transcriptase-polymerase chain reaction assay for these fusion transcripts. By incorporating consensus primers and gene-specific probes, both presence and subtype of the fusion were determined in one assay. We applied this approach to a convenience sample of 78 formalin-fixed, paraffin-embedded ARMS tumors from the Intergroup Rhabdomyosarcoma Study (IRS)-III clinical trial and obtained satisfactory results in 59 (76%) cases. The distribution of fusion types was 35 (59%) PAX3-FKHR, 11 (19%) PAX7-FKHR, and 13 fusion-negative (22%). In a subsequent clinical analysis, we found that IRS-III ARMS cases analyzed for fusion status had a significantly improved outcome compared to IRS-III ARMS cases that were not available for fusion analysis. The basis of this outcome could not be explained by known prognostic clinical factors, and multivariate analysis confirmed that our convenience sample was not representative of the whole IRS-III cohort. In conclusion, although these robust assays provide new opportunities for correlative studies of archival material, our first application illustrates an important limitation of using a convenience sample for molecular-clinical correlative studies.