A novel multifunctional oligonucleotide microarray for Toxoplasma gondii.
A novel multifunctional oligonucleotide microarray for Toxoplasma gondii.
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一种新型的多功能寡核苷酸微阵列，用于弓形虫Gondii。
DOI：
10.1186/1471-2164-11-603
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发表时间：
2010-10-25
期刊：
影响因子：
4.4
通讯作者：
Roos DS
中科院分区：
文献类型：
--
作者：
Bahl A;Davis PH;Behnke M;Dzierszinski F;Jagalur M;Chen F;Shanmugam D;White MW;Kulp D;Roos DS
微阵列是基因组询问、SNP检测和表达分析等应用的宝贵工具。这种广泛的能力将对许多病原体研究团体具有价值，尽管开发和使用基因组规模的微阵列通常是一项昂贵的工作。因此，在保持或扩展功能的同时减少不必要的探针的有效方法将与许多研究者相关。利用现有的弓形虫基因组序列和注释（一种导致免疫功能低下个体患病的致病寄生虫）和恶性疟原虫（一种导致严重人类疟疾的相关寄生虫），我们设计了一种能够以相对低的成本支持广泛应用的单一寡核苷酸微阵列，包括弓形虫的全基因组表达谱，和单核苷酸多态性（SNP）为基础的基因分型的T。弓形虫和恶性疟原虫。表达谱的三个克隆型谱系占主导地位的T。北美和欧洲的弓形虫种群提供了寄生虫转录组的第一个全面视图，揭示了所有注释基因的约49%在寄生虫速殖子中表达（负责发病的急性溶解阶段），26%的基因在菌株之间差异表达。一种新的设计，利用几个探针提供了高置信度的基因分型，在这里用来解决有性杂交的克隆后代中的重组点。最近的测序额外的T。弓形虫分离株鉴定了>620 K新的SNP，包括与表达谱探针交叉的~11 K，产生了用于基因分型研究的额外标记，并进一步验证了组合表达谱/基因分型阵列设计的实用性。促进SNP和转录本发现的其他应用，用于定量基因表达的替代统计方法等也在中试规模进行，以告知未来的阵列设计。除了提供T.由于弓形虫转录组跨越主要谱系，并允许详细解析历史有性杂交中的重组点，该阵列的多功能性质也允许将探针用于其预期用途以外的目的，从而增强分析。这个数组被T.弓形虫研究界，和几个方面的设计策略可能是有益的其他病原体。
Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators. Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals) and Plasmodium falciparum (a related parasite responsible for severe human malaria), we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP)-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis) and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at pilot scale to inform future array designs. In addition to providing an initial global view of the T. gondii transcriptome across major lineages and permitting detailed resolution of recombination points in a historical sexual cross, the multifunctional nature of this array also allowed opportunities to exploit probes for purposes beyond their intended use, enhancing analyses. This array is in widespread use by the T. gondii research community, and several aspects of the design strategy are likely to be useful for other pathogens.
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影响因子：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
6.7
作者：
Ganesan K;Ponmee N;Jiang L;Fowble JW;White J;Kamchonwongpaisan S;Yuthavong Y;Wilairat P;Rathod PK
通讯作者：
Rathod PK
影响因子：
12.3
作者：
Dharia NV;Sidhu AB;Cassera MB;Westenberger SJ;Bopp SE;Eastman RT;Plouffe D;Batalov S;Park DJ;Volkman SK;Wirth DF;Zhou Y;Fidock DA;Winzeler EA
通讯作者：
Winzeler EA
影响因子：
9.8
作者：
Bozdech, Zbynek;Llinas, Manuel;Pulliam, Brian Lee;Wong, Edith D;Zhu, Jingchun;DeRisi, Joseph L
通讯作者：
DeRisi, Joseph L
影响因子：
4.4
作者：
Jiang H;Yi M;Mu J;Zhang L;Ivens A;Klimczak LJ;Huyen Y;Stephens RM;Su XZ
通讯作者：
Su XZ