SNP基因芯片结合多重置换扩增技术检测单细胞非整倍体的研究

Detection of Aneuploidy from Single Cells by Array-Comparative Genetic Hybridization

【目的】建立并优化利用微阵列-比较基因组杂交技术检测单细胞非整倍体的实验方案。【方法】纤维母细胞系GM02732(47,XY,+18)和GM00343[46,XY,4(del)(qter>p14)]被用于实验。阳性对照组为上述细胞系的基因组DNA(gDNA)(A组与B组,n=6);实验组为单细胞模板的多重置换扩增(MDA)产物(C组与D组,n=10);阴性对照组为空白对照的MDA产物(E组,n=6)。以上样本与10k2.0基因分型芯片杂交并进行染色体拷贝数分析,比较利用非扩增的正常gDNA和同法扩增的DNA(MDA-DNA)作为分析参照对C组和D组的结果准确度的影响。【结果】A→E组的芯片杂交信号判读率分别为98.7%、97.2%、86.7%、85.9%与3.2%。利用单细胞MDA-DNA作为参照时,C组与D组杂交信号的变异程度明显小于使用gDNA作为参照时(P<0.05)。利用CNAT分析软件,发现以gDNA作为参照时,C组与D组部分染色体优势扩增明显,而使用MDA-DNA作为参照时则未观察到类似现象。【结论】结合MDA和基因芯片平台对单细胞进行非整倍体检测时应使用同法扩增的DNA作为分析参照。

[Objective] To set up an optimized protocol for aneuploidy detection from single cells through Array- Comparative Genetic Hybridization （CGH）. [Method] Two cell lines, trisomy 18 （Tri-18; GM02732, 47,XY, ＋18） and chromosome 4 segment deletion [sDel-4; GM00343, 46,XY,4（del） （qter 〉 p14）], were used in the study. In combination of 10 k 2.0 SNP mapping array platform and multiple displacement amplification （MDA）, the diagnostic accurate rates of MDA product from single cells of the two cell lines using gDNA and single-cell MDA product as reference were compared. [Result] An extremely lower call rate （3.2 ± 1.2）% in the negative control group was observed compared to the experiment groups. When the single-cell MDA product was used as reference, the standard deviations of Log2 （signal intensity ratio） were significantly decreased in both groups, compared with when the gDNA as reference （P = 0.004）. Through CNAT analytic software, some specific chromosomes （16, 17, 19, and 22） presented obvious preferential amplification （PA） when the gDNA was used as reference, but this PA could be eliminated when single-cell MDA product was used as reference. [Conclusion] 10 k 2.0 SNP mapping array in combination with MDA could be a quick, highly efficient and accurate method to detect aneuploidy in single cells.