Array-based comparative genomic hybridization for the detection of DNA sequence copy number changes in Barrett's adenocarcinoma
Array-based comparative genomic hybridization for the detection of DNA sequence copy number changes in Barrett's adenocarcinoma
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DOI：
10.1002/path.1576
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发表时间：
2004-07-01
影响因子：
7.3
通讯作者：
Walch, A
中科院分区：
文献类型：
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作者：
Albrecht, B;Hausmann, M;Walch, A
基于阵列的比较基因组杂交（aCGH）可以通过将差异标记的测试和对照DNA与基因组克隆微阵列共杂交，以高分辨率鉴定DNA序列拷贝数变化。本研究通过aCGH对23例Barrett腺癌（BCA, n = 18）和非肿瘤性食管鳞状上皮（n = 2）和贲门粘膜（n = 3）的福尔马林固定、石蜡包埋组织样本进行了分析。所使用的微阵列包含287个基因组靶点，包括癌基因、肿瘤抑制基因和先前报道在BCA中发生改变的染色体区域内的DNA序列。鉴定了大约50个基因的DNA序列拷贝数变化，其中大多数先前未在BCA中描述。DNA序列拷贝数增加（平均41 +/- 25/BCA）比DNA序列拷贝数损失（平均20 +/- 15/BCA）更频繁。SNRPN的DNA序列拷贝数增加频率最高（61%）；Gnly (44%)；Nme1 (44%)；DDX15、ABCB1 （MDR）、ATM、LAMA3、MYBL2、ZNF217、TNFRSF6B各占39%；MSH2、TERC、SERPINE1、AFM137XA11、IGF1R和PTPN1各占33%。PDGFB的DNA序列拷贝数丢失（44%）；D17S125 (39%);AKT3 (28%);RASSFI、FHIT、CDKN2A （p16）和SAS （CDK4）各占28%。在所有食管和贲门粘膜鳞状非肿瘤性组织样本中，测量的平均比值为1.00（食管鳞状粘膜）或1.01（胃粘膜），表明不存在DNA序列拷贝数机会。为了验证，选择aCGH检测到的克隆（SNRPN、CMYC、HER2、ZNF217），用荧光原位杂交（FISH）证实DNA序列拷贝数的变化。这些数据显示了aCGH对BCA DNA序列拷贝数变化的高分辨率识别的敏感性。新发现的基因可能包括BCA中迄今未知的生物标志物，因此是进一步研究阐明其在巴雷特癌发生中的可能作用的起点。版权所有(C) 2004大不列颠和爱尔兰病理学会。约翰威利之子有限公司出版。
Array-based comparative genomic hybridization (aCGH) allows the identification of DNA sequence copy number changes at high resolution by co-hybridizing differentially labelled test and control DNAs to a micro-array of genomic clones. The present study has analysed a series of 23 formalin-fixed, paraffin wax-embedded tissue samples of Barrett's adenocarcinoma (BCA, n = 18) and non-neoplastic squamous oesophageal (n = 2) and gastric cardia mucosa (n = 3) by aCGH. The micro-arrays used contained 287 genomic targets covering oncogenes, tumour suppressor genes, and DNA sequences localized within chromosomal regions previously reported to be altered in BCA. DNA sequence copy number changes for a panel of approximately 50 genes were identified, most of which have not been previously described in BCA. DNA sequence copy number gains (mean 41 +/- 25/BCA) were more frequent than DNA sequence copy number losses (mean 20 +/- 15/BCA). The highest frequencies for DNA sequence copy number gains were detected for SNRPN (61%); GNLY (44 %); NME1 (44 %); DDX15, ABCB1 (MDR), ATM, LAMA3, MYBL2, ZNF217, and TNFRSF6B (39 % each); and MSH2, TERC, SERPINE1, AFM137XA11, IGF1R, and PTPN1 (33% each). DNA sequence copy number losses were identified for PDGFB (44%); D17S125 (39%); AKT3 (28%); and RASSFI, FHIT, CDKN2A (p16), and SAS (CDK4) (28% each). In all non-neoplastic tissue samples of squamous oesophageal and gastric cardia mucosa, the measured mean ratios were 1.00 (squamous oesophageal mucosa) or 1.01 (gastric mucosa), indicating that no DNA sequence copy number chances were present. For validation, the DNA sequence copy number changes of selected clones (SNRPN, CMYC, HER2, ZNF217) detected by aCGH were confirmed by fluorescence in situ hybridization (FISH). These data show the sensitivity of aCGH for the identification of DNA sequence copy number changes at high resolution in BCA. The newly identified genes may include so far unknown biomarkers in BCA and are therefore a starting point for further studies elucidating their possible role in Barrett's carcinogenesis. Copyright (C) 2004 Pathological Society of Great Britain and Ireland. Published by John Wiley Sons, Ltd.