In silico phenotypic screening method of mutants based on statistical modeling of genetically mixed samples.
In comprehensive functional genomics projects, systematic analysis of phenotypes is vital. However, conventional phenotypic screening is done mainly by imprecise visual observation of qualitative traits, and, therefore, in silico screening techniques for quantitative traits are required. In this report, we propose in silico phenotypic screening method that utilizes a Gaussian mixture model for the trait distribution in the offspring of a mutagenized line and the likelihood ratio test between the estimated Gaussian mixture model and the wild-type single Gaussian model. In order to evaluate the proposed method, we performed a screening experiment using real trait data of Arabidopsis. In this experiment, the proposed screening method properly distinguished the mutant line from the wild-type line. Furthermore, we conducted power analysis of the proposed method and two conventional methods under various simulated conditions of sample size and distribution of trait frequency. The result of the power analysis confirmed the effectiveness of the proposed method compared to the conventional methods.
Kaminuma
Eli
E
Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan. eli@gsc.riken.jp
Heida
Naohiko
N
Yoshizumi
Takeshi
T
Nakazawa
Miki
M
Matsui
Minami
M
Toyoda
Tetsuro
T
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D005820:Genetic Testing / Q000379:methods; D014644:Genetic Variation / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods