High-density oligonucleotide array with sub-kilobase resolution reveals breakpoint information of submicroscopic deletions in nevoid basal cell carcinoma syndrome
High-density oligonucleotide array with sub-kilobase resolution reveals breakpoint information of submicroscopic deletions in nevoid basal cell carcinoma syndrome
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DOI：
10.1007/s00439-007-0419-y
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发表时间：
2007-12-01
期刊：
影响因子：
5.3
通讯作者：
Miyashita, Toshiyuki
中科院分区：
文献类型：
--
作者：
Fujii, Katsunori;Ishikawa, Shumpei;Miyashita, Toshiyuki
小的亚显微基因组缺失和重复占人类单基因疾病所有突变的15%。在这项研究中，我们使用新设计的高分辨率寡核苷酸微阵列，探针之间的中位数距离为776 bp（平均探针间隔2,271 bp），检测痣样基底细胞癌综合征（NBCCS）患者的基因缺失。NBCCS，也称为Gorlin综合征，其特征在于由人类patched-1（PTCH 1）基因突变引起的发育缺陷和肿瘤发生，如髓母细胞瘤和基底细胞癌。三分之二的缺失不能通过常规染色体分析检测到。检测到小至165 kb的亚显微缺失，仅影响PTCH 1，而其他两个缺失大得多（5和11 Mb）。我们不仅证明了参与缺失的基因的确切数量，而且在所有分析的个体中精确定位断点区域后快速确定了连接序列。这份基于阵列的长缺失连接序列测定报告规避了劳动密集型分析，如Southern印迹或FISH。在一种情况下，在其他两种情况下，非同源末端连接的cDNA介导的重组可能涉及在产生的缺失。该方法将有助于理解基因缺失的分子发病机制以及快速基因检测。
Small submicroscopic genomic deletions and duplications constitute up to 15% of all mutations underlying human monogenic diseases. In this study, we used newly designed high-resolution oligonucleotide microarrays with a median distance between the probes of 776 bp (average probe interval 2,271 bp) to detect gene deletions in nevoid basal cell carcinoma syndrome (NBCCS) patients. NBCCS, also called Gorlin syndrome, is characterized by developmental defects and tumorigenesis such as medulloblastomas and basal cell carcinomas, caused by mutations of the human patched-1 (PTCH1) gene. Two out of three deletions could not be detected by a conventional chromosomal analysis. A submicroscopic deletion as small as 165 kb was detected affecting only PTCH1, whereas the other two deletions were much larger (5 and 11 Mb). We demonstrated not only the exact number of genes involved in the deletion but also rapidly determined the junction sequences after pinpointing the breakpoint regions in all individuals analyzed. This report of an array-based determination of junction sequences of long deletions circumvented a labor-intensive analysis such as Southern blotting or FISH. Alu-mediated recombination in one case and non-homologous end joining in the other two were probably implicated in the generation of deletions. This method will contribute to the understanding of molecular pathogenesis of gene deletions as well as rapid genetic testing.