Selective Phenotyping, Entropy Reduction, and the Mastermind game

BMC Bioinformatics

Research Article

Julien Gagneur¹  Achim Tresch²  Markus C Elze³ 

[1] European Molecular Biology Lab, 69122, Heidelberg, Germany;Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany;Johannes Gutenberg-University, 55099Mainz, Germany;

关键词: Quantitative Trait Locus;    Recombinant Inbred Line;    Quantitative Trait Locus Mapping;    Quantitative Trait Locus Effect;    Quantitative Trait Locus Interval;   

DOI  :  10.1186/1471-2105-12-406

 received in 2011-04-01, accepted in 2011-10-20,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundWith the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately.ResultsHere we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset.ConclusionsUsing entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping.

【 授权许可】

CC BY   
© Gagneur et al; licensee BioMed Central Ltd. 2011