应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Detection of a copy number mutation on chromosome 7q36 using the Affymetrix SNP Array 6.0

目的 应用Affymetrix全基因组芯片结合荧光定量PCR（quantitative real-timePCR，qPCR）技术，进行致病性DNA拷贝数变异的精细定位研究。方法以一个定位于染色体7q36的中国人遗传性三节拇指多并指综合征伴随Ⅳ型并指家系中的一例患者为研究对象。收集外周血标本，常规提取基因组DNA。应用Affymetrix Genome-Wide Human SNP Array6．0芯片，将基因组DNA纯化，经过酶切、连接、扩增、标记、杂交、染色和扫描等步骤后得到原始数据，应用Affymetrix Genotyping Console3．0软件进行拷贝数分析。在经芯片分析所确定的重复范围内设计引物，采用qPCR方法进行验证，并进一步缩小断端范周、精确重复区域范围。结果将患者重复区域两断端范围由原来的113kb和33kb分别缩小到5．4kb和1．8kb，致病性DNA重复范围由原来的291～437kb精确至379～387kb。结论应用Affymetrix全基因组芯片联合qPCR技术可以实现对DNA拷贝数突变的精确、可靠的检测。

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndactyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR （qPCR）. Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.