Lucito Robert, Healy John, Alexander Joan, Reiner Andrew, Esposito Diane, Chi Maoyen, Rodgers Linda, Brady Amy, Sebat Jonathan, Troge Jennifer, West Joseph A, Rostan Seth, Nguyen Ken C Q, Powers Scott, Ye Kenneth Q, Olshen Adam, Venkatraman Ennapadam, Norton Larry, Wigler Michael
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Genome Res. 2003 Oct;13(10):2291-305. doi: 10.1101/gr.1349003. Epub 2003 Sep 15.
We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with "representations" from cancer and normal cells, we detect regions of the genome with altered "copy number." We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.
我们开发了一种名为ROMA（代表性寡核苷酸微阵列分析）的方法，用于检测癌症患者和正常人体内的基因组畸变。通过将根据人类基因组序列设计的寡核苷酸探针进行阵列排列，并与癌症细胞和正常细胞的“代表性片段”杂交，我们能够检测到基因组中“拷贝数”发生改变的区域。我们在整个基因组中实现了平均30 kb的分辨率，并且每15 kb设置一个探针的高分辨率也是可行的。我们阐述了阵列上探针的特性以及使用ROMA获得的测量结果的准确性。利用这种方法，我们识别出癌症基因组与正常基因组之间以及正常人类基因组之间的差异。在癌症基因组中，我们能够轻易检测到扩增以及大小不同的纯合和半合子缺失。在正常人类基因组之间，我们经常检测到大片段（100 kb至1 Mb）的缺失或重复。其中许多变化涉及已知基因。ROMA将有助于发现对癌症至关重要的基因和标记，以及可能对疾病遗传易感性具有重要意义的基因座。
