An optimized procedure for the design and evaluation of Ecotilling assays.
An optimized procedure for the design and evaluation of Ecotilling assays.
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DOI：
10.1186/1471-2164-9-510
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发表时间：
2008-10-30
期刊：
影响因子：
4.4
通讯作者：
Kronenberg F
中科院分区：
文献类型：
--
作者：
Coassin S;Brandstätter A;Kronenberg F
单核苷酸多态性（SNPs）是人类基因组中最常见的遗传变异形式，在表型遗传率中起着重要作用。频率低于5%的特别罕见的等位基因可能对复杂疾病的发展表现出特别强的影响。通过标准DNA测序检测稀有等位基因是耗时且成本密集的。在这里，我们讨论了一种替代方法，用于高通量检测罕见的突变，在大的人口样本中使用嵌入在生物信息学分析工具的集合中的Ecotilling。Ecotilling最初作为TILLING引入，用于筛选植物中罕见的化学诱导突变，后来用于人类样本，显示出对人类罕见等位基因检测的出色适用性。在没有生物信息学支持的情况下，使用Ecotilling进行人类大型突变筛查项目的实际问题是缺乏快速而全面地评估每个新发现的变异并将其置于正确的基因组背景中的解决方案。我们提出了一个优化的策略，设计，评价和解释生态耕作的结果，通过整合几个主要是免费提供的生物信息学工具。我们的调查的一个主要重点是评估和有意义的经济组合，这些软件工具的推断不同的可能的监管功能，每个新检测到的突变。我们的简化程序大大促进了Ecotilling检测的实验设计和评估，并大大改善了优先考虑新发现的SNP进行进一步下游分析的决策过程。
Single nucleotide polymorphisms (SNPs) are the most common form of genetic variability in the human genome and play a prominent role in the heritability of phenotypes. Especially rare alleles with frequencies less than 5% may exhibit a particularly strong influence on the development of complex diseases. The detection of rare alleles by standard DNA sequencing is time-consuming and cost-intensive. Here we discuss an alternative approach for a high throughput detection of rare mutations in large population samples using Ecotilling embedded in a collection of bioinformatic analysis tools. Ecotilling originally was introduced as TILLING for the screening for rare chemically induced mutations in plants and later adopted for human samples, showing an outstanding suitability for the detection of rare alleles in humans. An actual problem in the use of Ecotilling for large mutation screening projects in humans without bioinformatic support is represented by the lack of solutions to quickly yet comprehensively evaluate each newly found variation and place it into the correct genomic context. We present an optimized strategy for the design, evaluation and interpretation of Ecotilling results by integrating several mostly freely available bioinformatic tools. A major focus of our investigations was the evaluation and meaningful economical combination of these software tools for the inference of different possible regulatory functions for each newly detected mutation. Our streamlined procedure significantly facilitates the experimental design and evaluation of Ecotilling assays and strongly improves the decision process on prioritizing the newly found SNPs for further downstream analysis.
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DOI：
10.1056/nejmoa072366
发表时间：
2007-08-02
期刊：
The New England journal of medicine
影响因子：
--
作者：
Samani NJ;Erdmann J;Hall AS;Hengstenberg C;Mangino M;Mayer B;Dixon RJ;Meitinger T;Braund P;Wichmann HE;Barrett JH;König IR;Stevens SE;Szymczak S;Tregouet DA;Iles MM;Pahlke F;Pollard H;Lieb W;Cambien F;Fischer M;Ouwehand W;Blankenberg S;Balmforth AJ;Baessler A;Ball SG;Strom TM;Braenne I;Gieger C;Deloukas P;Tobin MD;Ziegler A;Thompson JR;Schunkert H;WTCCC and the Cardiogenics Consortium
通讯作者：
WTCCC and the Cardiogenics Consortium
影响因子：
14.9
作者：
Oleykowski, CA;Mullins, CRB;Yeung, AT
通讯作者：
Yeung, AT
影响因子：
64.5
作者：
Lewis, BP;Shih, IH;Burge, CB
通讯作者：
Burge, CB
TransFac及其模块移植：真核生物中的转录基因调节。
影响因子：
14.9
作者：
Matys V;Kel-Margoulis OV;Fricke E;Liebich I;Land S;Barre-Dirrie A;Reuter I;Chekmenev D;Krull M;Hornischer K;Voss N;Stegmaier P;Lewicki-Potapov B;Saxel H;Kel AE;Wingender E
通讯作者：
Wingender E
影响因子：
5.8
作者：
Cartharius, K;Frech, K;Werner, T
通讯作者：
Werner, T