Glioma test array for use with formalin-fixed, paraffin-embedded tissue - Array comparative genomic hybridization correlates with loss of heterozygosity and fluorescence in situ hybridization
Glioma test array for use with formalin-fixed, paraffin-embedded tissue - Array comparative genomic hybridization correlates with loss of heterozygosity and fluorescence in situ hybridization
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DOI：
10.2353/jmoldx.2006.050109
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发表时间：
2006-05-01
影响因子：
4.1
通讯作者：
Louis, David N.
中科院分区：
文献类型：
--
作者：
Mohapatra, Gayatry;Betensky, Rebecca A.;Louis, David N.
基于阵列的比较基因组杂交(ACGH)是一种强大的、高通量的全基因组分析工具。直到最近，aCGH只能在冷冻组织样本和大量组织样本上重复进行。然而，对于脑肿瘤，来自小型立体定向活检的石蜡包埋组织块可能是唯一常规可用的组织。因此，分析福尔马林固定、石蜡包埋(FFPE)材料的方法的发展有可能对分子诊断产生重大影响。为此，我们构建了代表1、7、19和X染色体的BAC阵列，因为1p/19q缺失和EGFR基因扩增为胶质瘤的诊断提供了临床相关信息。我们还优化了使用胺修饰的核苷酸来产生aCGH探针的两步标记程序。应用这种方法，我们分析了一系列28例FFPE少突胶质细胞肿瘤的1、7和19号染色体的改变，并通过荧光原位杂交和杂合性丢失分析独立地检测了这些肿瘤的1p/19q缺失。在分析的染色体中，aCGH、标准杂合性损失和荧光原位杂交的符合率接近100%。这些结果表明，aCGH可以为胶质瘤提供一种改进的分子诊断方法，因为它能够在小的FFPE标本中检测临床相关的分子变化。
Array-based comparative genomic hybridization (aCGH) is a powerful, high-throughput tool for whole genome analysis. Until recently, aCGH could only be reproducibly performed on frozen tissue samples and with significant tissue amounts. For brain tumors however, paraffin-embedded tissue blocks from small stereotactic biopsies may be the only tissue routinely available. The development of methods to analyze formalin-fixed, paraffin-embedded (FFPE) material therefore has the potential to impact molecular diagnosis in a significant way. To this end, we constructed a BAC array representing chromosomes 1, 7, 19, and X because 1p/19q deletion and EGFR gene amplification provide clinically relevant information for glioma diagnosis. We also optimized a two-step labeling procedure using an amine-modified nucleotide for generating aCGH probes. Using this approach, we analyzed a series of 28 FFPE oligodendroglial tumors for alterations of chromosomes 1, 7, and 19. We also independently assayed these tumors for 1p/19q deletion by fluorescence in situ hybridization and by loss of heterozygosity analyses. The concordance between aCGH, standard loss of heterozygosity and fluorescence in situ hybridization was nearly 100% for the chromosomes analyzed. These results suggest that aCGH could offer an improved molecular diagnostic approach for gliomas because of its ability to detect clinically relevant molecular alterations in small FFPE specimens.