Robust and sensitive analysis of mouse knockout phenotypes.
Robust and sensitive analysis of mouse knockout phenotypes.
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DOI：
10.1371/journal.pone.0052410
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Mott RF
中科院分区：
文献类型：
--
作者：
Karp NA;Melvin D;Sanger Mouse Genetics Project;Mott RF
体内研究的一个重大挑战是用稳健可靠的方法鉴定表型。挑战来自于实际问题，导致实验设计并不理想。育种问题，特别是在存在生育力或繁殖力问题的情况下，经常导致多批次收集数据。这个问题在高通量表型分型程序中是严重的。此外，在高通量环境中，操作问题导致控制不与敲除在同一天测量。我们强调如何应用传统的方法，如学生的t检验或双向方差分析，在这些情况下给出有缺陷的结果，不应该使用。我们使用来自桑格小鼠基因组计划的工作实例探索混合模型的使用，重点是用于分析小鼠敲除数据的双能X射线吸收测定数据，并与参考范围方法进行比较。我们表明，混合模型分析更敏感，更不容易出现人为因素，从而发现基因功能与人类疾病相关的微妙定量表型。我们演示了混合模型方法如何具有能够包括协变量（如体重）的额外优势，以将基因型的影响与这些协变量分开。这是基因敲除研究中的一个特殊问题，其中体重是常见的表型，并将提高分配表型和随后选择用于次级表型的品系的精度。使用混合模型与体内研究不仅在提高数据分析的质量和灵敏度方面具有价值，而且在伦理上作为一种适合于小批量的方法，减少了菌落的繁殖负担。这将减少动物的使用，增加产量，降低成本，同时提高所获得知识的质量和深度。
A significant challenge of in-vivo studies is the identification of phenotypes with a method that is robust and reliable. The challenge arises from practical issues that lead to experimental designs which are not ideal. Breeding issues, particularly in the presence of fertility or fecundity problems, frequently lead to data being collected in multiple batches. This problem is acute in high throughput phenotyping programs. In addition, in a high throughput environment operational issues lead to controls not being measured on the same day as knockouts. We highlight how application of traditional methods, such as a Student’s t-Test or a 2-way ANOVA, in these situations give flawed results and should not be used. We explore the use of mixed models using worked examples from Sanger Mouse Genome Project focusing on Dual-Energy X-Ray Absorptiometry data for the analysis of mouse knockout data and compare to a reference range approach. We show that mixed model analysis is more sensitive and less prone to artefacts allowing the discovery of subtle quantitative phenotypes essential for correlating a gene’s function to human disease. We demonstrate how a mixed model approach has the additional advantage of being able to include covariates, such as body weight, to separate effect of genotype from these covariates. This is a particular issue in knockout studies, where body weight is a common phenotype and will enhance the precision of assigning phenotypes and the subsequent selection of lines for secondary phenotyping. The use of mixed models with in-vivo studies has value not only in improving the quality and sensitivity of the data analysis but also ethically as a method suitable for small batches which reduces the breeding burden of a colony. This will reduce the use of animals, increase throughput, and decrease cost whilst improving the quality and depth of knowledge gained.
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影响因子：
48
作者：
Richter, S. Helene;Garner, Joseph P.;Wuerbel, Hanno
通讯作者：
Wuerbel, Hanno
影响因子：
78.5
作者：
Ransohoff, DF
通讯作者：
Ransohoff, DF
DOI：
10.1152/ajpendo.00470.2002
发表时间：
2003-09-01
影响因子：
5.1
作者：
Brommage, R
通讯作者：
Brommage, R
影响因子：
3.7
作者：
Kilkenny C;Parsons N;Kadyszewski E;Festing MF;Cuthill IC;Fry D;Hutton J;Altman DG
通讯作者：
Altman DG
影响因子：
2.5
作者：
Cook, Melloni N.;Dunning, Jonathan P.;Goldowitz, Dan
通讯作者：
Goldowitz, Dan