A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity.
A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity.
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DOI：
10.1186/1471-2164-15-719
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发表时间：
2014-08-26
期刊：
影响因子：
4.4
通讯作者：
Plowe CV
中科院分区：
文献类型：
--
作者：
Jacob CG;Tan JC;Miller BA;Tan A;Takala-Harrison S;Ferdig MT;Plowe CV
来自全基因组研究的单核苷酸多态性（SNPs）分析允许快速评估全基因组多样性，恶性疟原虫的基因组流行病学研究提供了对寄生虫种群结构，基因流，耐药性和疫苗开发的见解。在有足够冷链设施的地区，可以冷冻大量去除白细胞的患者血液，用于寄生虫基因组分析。在较偏远的流行地区，用手指刺破少量受感染的血液，干燥后储存在滤纸上。这些干燥的血斑通常不能产生足够浓缩的寄生虫DNA用于全基因组测序。设计了一种DNA微阵列，用于对田间样品进行全基因组SNP分型，先前的测序显示这些SNP在非洲、东南亚和巴布亚新几内亚是可变的。设计了一种算法来调用具有低寄生虫DNA的样品中的SNP。使用这种新算法，通过杂交来自疟疾实验室菌株的纯化DNA，并将调用与来自全基因组序列的SNP进行比较，测得SNP调用准确率为98%。从东南亚研究中收集的疟疾现场样本中提取的DNA的平均准确率也达到了98%以上，平均调用率为82%以上。这种新的高密度微阵列提供了来自广泛寄生虫DNA量的高质量SNP调用，并代表了在不同环境中进行疟疾寄生虫全基因组分析的强大工具。
Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In areas with adequate cold chain facilities, large volumes of leukocyte-depleted patient blood can be frozen for use in parasite genomic analyses. In more remote endemic areas smaller volumes of infected blood are taken by finger prick, and dried and stored on filter paper. These dried blood spots do not generally yield enough concentrated parasite DNA for whole-genome sequencing. A DNA microarray was designed for use on field samples to type a genome-wide set of SNPs which prior sequencing had shown to be variable in Africa, Southeast Asia, and Papua New Guinea. An algorithm was designed to call SNPs in samples with low parasite DNA. With this new algorithm SNP-calling accuracy of 98% was measured by hybridizing purified DNA from malaria lab strains and comparing calls with SNPs called from full genome sequences. An average accuracy of >98% was likewise obtained for DNA extracted from malaria field samples collected in studies in Southeast Asia, with an average call rate of > 82%. This new high-density microarray provided high quality SNP calls from a wide range of parasite DNA quantities, and represents a robust tool for genome-wide analysis of malaria parasites in diverse settings.
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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：
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
影响因子：
2.1
作者：
Carvalho, Benilton;Bengtsson, Henrik;Irizarry, Rafael A.
通讯作者：
Irizarry, Rafael A.
DOI：
10.1056/nejmp1108322
发表时间：
2011-09-22
期刊：
The New England journal of medicine
影响因子：
--
作者：
Dondorp AM;Fairhurst RM;Slutsker L;Macarthur JR;Breman JG;Guerin PJ;Wellems TE;Ringwald P;Newman RD;Plowe CV
通讯作者：
Plowe CV
DOI：
10.1073/pnas.1211205110
发表时间：
2013-01-02
影响因子：
11.1
作者：
Takala-Harrison, Shannon;Clark, Taane G.;Plowe, Christopher V.
通讯作者：
Plowe, Christopher V.