scholarly journals Functional Mapping of Multiple Dynamic Traits

Author(s):  
Jiguo Cao ◽  
Liangliang Wang ◽  
Zhongwen Huang ◽  
Junyi Gai ◽  
Rongling Wu
2016 ◽  
Vol 2016 ◽  
pp. 1-13
Author(s):  
Jiandong Qi ◽  
Jianfeng Sun ◽  
Jianxin Wang

While it is a daunting challenge in current biology to understand how the underlying network of genes regulates complex dynamic traits, functional mapping, a tool for mapping quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs), has been applied in a variety of cases to tackle this challenge. Though useful and powerful, functional mapping performs well only when one or more model parameters are clearly responsible for the developmental trajectory, typically being a logistic curve. Moreover, it does not work when the curves are more complex than that, especially when they are not monotonic. To overcome this inadaptability, we therefore propose a mathematical-biological concept and measurement,E-index (earliness-index), which cumulatively measures the earliness degree to which a variable (or a dynamic trait) increases or decreases its value. Theoretical proofs and simulation studies show thatE-index is more general than functional mapping and can be applied to any complex dynamic traits, including those with logistic curves and those with nonmonotonic curves. Meanwhile,E-index vector is proposed as well to capture more subtle differences of developmental patterns.


2011 ◽  
Vol 27 (14) ◽  
pp. 2006-2008 ◽  
Author(s):  
Chunfa Tong ◽  
Zhong Wang ◽  
Bo Zhang ◽  
Jisen Shi ◽  
Rongling Wu

2010 ◽  
Vol 92 (1) ◽  
pp. 55-62 ◽  
Author(s):  
TIANBO JIN ◽  
JIAHAN LI ◽  
YING GUO ◽  
XIAOJING ZHOU ◽  
RUNQING YANG ◽  
...  

SummaryAs an emerging powerful approach for mapping quantitative trait loci (QTLs) responsible for dynamic traits, functional mapping models the time-dependent mean vector with biologically meaningful equations and are likely to generate biologically relevant and interpretable results. Given the autocorrelation nature of a dynamic trait, functional mapping needs the implementation of the models for the structure of the covariance matrix. In this article, we have provided a comprehensive set of approaches for modelling the covariance structure and incorporated each of these approaches into the framework of functional mapping. The Bayesian information criterion (BIC) values are used as a model selection criterion to choose the optimal combination of the submodels for the mean vector and covariance structure. In an example for leaf age growth from a rice molecular genetic project, the best submodel combination was found between the Gaussian model for the correlation structure, power equation of order 1 for the variance and the power curve for the mean vector. Under this combination, several significant QTLs for leaf age growth trajectories were detected on different chromosomes. Our model can be well used to study the genetic architecture of dynamic traits of agricultural values.


Heredity ◽  
2008 ◽  
Vol 101 (4) ◽  
pp. 321-328 ◽  
Author(s):  
W Hou ◽  
H Li ◽  
B Zhang ◽  
M Huang ◽  
R Wu

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e24902 ◽  
Author(s):  
Cen Wu ◽  
Gengxin Li ◽  
Jun Zhu ◽  
Yuehua Cui

2020 ◽  
Vol 132 (4) ◽  
pp. 1017-1023 ◽  
Author(s):  
Bryan D. Choi ◽  
Daniel K. Lee ◽  
Jimmy C. Yang ◽  
Caroline M. Ayinon ◽  
Christine K. Lee ◽  
...  

OBJECTIVEIntraoperative seizures during craniotomy with functional mapping is a common complication that impedes optimal tumor resection and results in significant morbidity. The relationship between genetic mutations in gliomas and the incidence of intraoperative seizures has not been well characterized. Here, the authors performed a retrospective study of patients treated at their institution over the last 12 years to determine whether molecular data can be used to predict the incidence of this complication.METHODSThe authors queried their institutional database for patients with brain tumors who underwent resection with intraoperative functional mapping between 2005 and 2017. Basic clinicopathological characteristics, including the status of the following genes, were recorded: IDH1/2, PIK3CA, BRAF, KRAS, AKT1, EGFR, PDGFRA, MET, MGMT, and 1p/19q. Relationships between gene alterations and intraoperative seizures were evaluated using chi-square and two-sample t-test univariate analysis. When considering multiple predictive factors, a logistic multivariate approach was taken.RESULTSOverall, 416 patients met criteria for inclusion; of these patients, 98 (24%) experienced an intraoperative seizure. Patients with a history of preoperative seizure and those treated with antiepileptic drugs prior to surgery were less likely to have intraoperative seizures (history: OR 0.61 [95% CI 0.38–0.96], chi-square = 4.65, p = 0.03; AED load: OR 0.46 [95% CI 0.26–0.80], chi-square = 7.64, p = 0.01). In a univariate analysis of genetic markers, amplification of genes encoding receptor tyrosine kinases (RTKs) was specifically identified as a positive predictor of seizures (OR 5.47 [95% CI 1.22–24.47], chi-square = 5.98, p = 0.01). In multivariate analyses considering RTK status, AED use, and either 2007 WHO tumor grade or modern 2016 WHO tumor groups, the authors found that amplification of the RTK proto-oncogene, MET, was most predictive of intraoperative seizure (p < 0.05).CONCLUSIONSThis study describes a previously unreported association between genetic alterations in RTKs and the occurrence of intraoperative seizures during glioma resection with functional mapping. Future models estimating intraoperative seizure risk may be enhanced by inclusion of genetic criteria.


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