Tan John C, Patel Jigar J, Tan Asako, Blain J Craig, Albert Tom J, Lobo Neil F, Ferdig Michael T
The Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA.
Genomics. 2009 Jun;93(6):543-50. doi: 10.1016/j.ygeno.2009.02.007. Epub 2009 Mar 11.
Microarray-based comparative genomic hybridizations (CGH) interrogate genomic DNA to identify structural differences such as amplifications and deletions that are easily detected as large signal aberrations. Subtle signal deviations caused by single nucleotide polymorphisms (SNPs) can also be detected but is challenged by a high AT content (81%) in P. falciparum. We compared genome-wide CGH signal to sequence polymorphisms between parasite strains 3D7, HB3, and Dd2 using NimbleGen microarrays. From 23,191 SNPs (excluding var/rif/stevor genes), our CGH probe set detected SNPs with >99.9% specificity but low (<10%) sensitivity. Probe length, melting temperature, GC content, SNP location in the probe, mutation type, and hairpin structures affected SNP sensitivity. Previously unrecognized variable number tandem repeats (VNTRs) also were detected by this method. These findings will guide the redesign of a probe set to optimize an openly available CGH microarray platform for high-resolution genotyping suitable for population genomics studies.
基于微阵列的比较基因组杂交（CGH）技术通过检测基因组DNA来识别结构差异，如扩增和缺失，这些差异很容易被检测为大的信号异常。单核苷酸多态性（SNP）引起的细微信号偏差也能被检测到，但由于恶性疟原虫的AT含量较高（81%），这一检测面临挑战。我们使用NimbleGen微阵列比较了寄生虫菌株3D7、HB3和Dd2之间全基因组CGH信号与序列多态性。在23,191个SNP（不包括var/rif/stevor基因）中，我们的CGH探针集检测SNP时特异性>99.9%，但灵敏度较低（<10%）。探针长度、解链温度、GC含量、探针中的SNP位置、突变类型和发夹结构会影响SNP的灵敏度。该方法还检测到了以前未被识别的可变数目串联重复序列（VNTR）。这些发现将指导探针集重新设计以优化一个公开可用的CGH微阵列平台，用于适合群体基因组学研究的高分辨率基因分型。
