Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray.
Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray.
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DOI：
10.1186/1471-2164-9-398
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发表时间：
2008-08-25
期刊：
影响因子：
4.4
通讯作者：
Su XZ
中科院分区：
文献类型：
--
作者：
Jiang H;Yi M;Mu J;Zhang L;Ivens A;Klimczak LJ;Huyen Y;Stephens RM;Su XZ
基因图谱是一种强大的方法，可以识别导致人类疟原虫恶性疟原虫耐药性和其他表型变化的突变。为了有效地定位靶基因，通常需要对大量多态性标记进行基因分型。目前，社区正在努力从寄生虫基因组中收集单核苷酸多态性 (SNP)。在这里，我们通过将微阵列的单特征多态性 (SFP) 调用与寄生虫分离株中已知的 SNP 进行比较，评估具有 256 万个探针的高密度“平铺”微阵列的多态性检测准确性。我们发现探针GC含量、探针中的SNP位置、探针覆盖度和信号比截止值是准确检测寄生虫基因组中SFP的重要因素。我们建立了一组可以高精度（≥ 94%）预测 mSFP（由多个重叠探针调用的 SFP）的 SFP 调用参数，并从 5 个寄生虫分离株中鉴定出全基因组范围内的 121,087 个 mSFP，其中包括 40,354 个独特的 mSFP（不包括来自多基因家族的 mSFP）和约 18,000 个新的 mSFP，生成了平均每 570 个寄生虫有一个独特的 mSFP 的遗传图谱。 bp。寄生虫之间的基因组拷贝数变异（CNV）也被编目和比较。使用高密度微阵列从恶性疟原虫基因组中发现了大量的mSFP，其中大多数位于染色体末端的高度多态性基因簇中。我们的准确 mSFP 检测方法和识别出的 mSFP 将极大地促进恶性疟原虫基因组变异的大规模研究，并为绘制重要寄生虫性状提供有用的资源。
Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite Plasmodium falciparum. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP) from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP) calls from the microarray with known SNP among parasite isolates. We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes) with high accuracy (≥ 94%) and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families) and ~18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV) among the parasites was also cataloged and compared. A large number of mSFP were discovered from the P. falciparum genome using a high-density microarray, most of which were in clusters of highly polymorphic genes at chromosome ends. Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the P. falciparum parasite and provide useful resources for mapping important parasite traits.
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影响因子：
30.8
作者：
Gunderson, KL;Steemers, FJ;Chee, MS
通讯作者：
Chee, MS
DOI：
10.1073/pnas.90.17.8292
发表时间：
1993-09-01
影响因子：
11.1
作者：
DAY, KP;KARAMALIS, F;KEMP, DJ
通讯作者：
KEMP, DJ
影响因子：
30.8
作者：
Buch, Stephan;Schafmayer, Clemens;Hampe, Jochen
通讯作者：
Hampe, Jochen
DOI：
10.1073/pnas.91.3.1143
发表时间：
1994-02-01
影响因子：
11.1
作者：
COWMAN, AF;GALATIS, D;THOMPSON, JK
通讯作者：
THOMPSON, JK
影响因子：
30.8
作者：
Mu, Jianbing;Awadalla, Philip;Su, Xin-zhuan
通讯作者：
Su, Xin-zhuan