A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects

2004 ◽  
Vol 3 (1) ◽  
pp. 1-27 ◽  
Author(s):  
Christoph Lange ◽  
Kristel van Steen ◽  
Toby Andrew ◽  
Helen Lyon ◽  
Dawn L DeMeo ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Software Package ◽  
Quantitative Traits ◽  
Univariate Analysis ◽  
Principal Component ◽  
Genetic Effects ◽  
Association Test ◽  
Practical Relevance ◽  
Simulation Studies ◽  
Family Based

We propose a family-based association test, FBAT-PC, for studies with quantitative traits that are measured repeatedly. The traits may be influenced by partially or completely unknown factors that may vary for each measurement. Using generalized principal component analysis, FBAT-PC amplifies the genetic effects of each measurement by constructing an overall phenotype with maximal heritability. Analytically, and in the simulation studies, we compare FBAT-PC with standard methodology and assess both the heritability of the overall phenotype and the power of FBAT-PC. Compared to univariate analysis, FBAT-PC achieves power gains of up to 200%. Applications of FBAT-PC to an osteoporosis study and to an asthma study show the practical relevance of FBAT-PC. FBAT-PC has been implemented in the software package PBAT and is freely available at http://www.biostat.harvard.edu/~clange/default.htm.

Genetic association test based on principal component analysis

2017 ◽  
Vol 16 (3) ◽  
Author(s):  
Zhongxue Chen ◽  
Shizhong Han ◽  
Kai Wang
Keyword(s):  
Principal Component Analysis ◽  
Genetic Association ◽  
Rare Variants ◽  
Association Studies ◽  
Principal Component ◽  
Real Data ◽  
Component Analysis ◽  
Association Test ◽  
Simulation Studies ◽  
Special Case

AbstractMany gene- and pathway-based association tests have been proposed in the literature. Among them, the SKAT is widely used, especially for rare variants association studies. In this paper, we investigate the connection between SKAT and a principal component analysis. This investigation leads to a procedure that encompasses SKAT as a special case. Through simulation studies and real data applications, we compare the proposed method with some existing tests.

scholarly journals Principal Component Analysis of Some Quantitative and Qualitative Traits in Iranian Spinach Landraces

2017 ◽  
Vol 71 (4) ◽  
pp. 307-310
Author(s):  
Mehdi Mohebodini ◽  
Naser Sabaghnia ◽  
Farhad Behtash ◽  
Mohsen Janmohammadi
Keyword(s):  
Principal Component Analysis ◽  
Principal Components ◽  
Quantitative Traits ◽  
Agronomic Traits ◽  
Principal Component ◽  
Component Analysis ◽  
Leaf Width ◽  
Petiole Length ◽  
Qualitative Traits ◽  
Eigen Values

Abstract Landraces of spinach in Iran have not been sufficiently characterised for their morpho-agronomic traits. Such characterisation would be helpful in the development of new genetically improved cultivars. In this study 54 spinach accessions collected from the major spinach growing areas of Iran were evaluated to determine their phenotypic diversity profile of spinach genotypes on the basis of 10 quantitative and 9 qualitative morpho-agronomic traits. High coefficients of variation were recorded in some quantitative traits (dry yield and leaf area) and all of the qualitative traits. Using principal component analysis, the first four principal components with eigen-values more than 1 contributed 87% of the variability among accessions for quantitative traits, whereas the first four principal components with eigen-values more than 0.8 contributed 79% of the variability among accessions for qualitative traits. The most important relations observed on the first two principal components were a strong positive association between leaf width and petiole length; between leaf length and leaf numbers in flowering; and among fresh yield, dry yield and petiole diameter; a near zero correlation between days to flowering with leaf width and petiole length. Prickly seeds, high percentage of female plants, smooth leaf texture, high numbers of leaves at flowering, greygreen leaves, erect petiole attitude and long petiole length are important characters for spinach breeding programmes.

A strategy for selecting diverse accessions using Principal Component Analysis from a large germplasm collection of soybean

2003 ◽  
Vol 1 (2-3) ◽  
pp. 151-156 ◽  
Author(s):  
R. L Sapra ◽  
S. K. Lal
Keyword(s):  
Principal Component Analysis ◽  
Sample Size ◽  
Principle Component Analysis ◽  
Quantitative Traits ◽  
Germplasm Collection ◽  
Principal Component ◽  
Target Population ◽  
Component Analysis ◽  
Principle Component ◽  
The Individual

AbstractWe suggest a diversity-dependent strategy, based on Principle Component Analysis, for selecting distinct accessions/parents for breeding from a soybean germplasm collection comprising of 463 lines, characterized and evaluated for 10 qualitative and eight quantitative traits. A sample size of six accessions included all the three states, namely low, medium and high of the individual quantitative traits, while a sample of 16–19 accessions included all the 60–64 distinct states of qualitative as well as quantitative traits. Under certain assumptions, the paper also develops an expression for estimating the size of a target population for capturing maximum variability in a sample three accessions.

scholarly journals Morphoanatomical study of Matricaria L. (Asteraceae) in Turkey

2019 ◽  
Vol 43 (2) ◽  
pp. 151-159
Author(s):  
Huseyin Inceer ◽  
Murat Bal
Keyword(s):  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Multivariate Analysis ◽  
Analysis Of Variance ◽  
Univariate Analysis ◽  
Principal Component ◽  
New Information ◽  
Turkish Flora ◽  
Pericarp Thickness ◽  
Diagnostic Traits

In the Turkish flora, the genus Matricaria is present with four taxa, namely M. aurea, M. chamomilla var. chamomilla, M. chamomilla var. recutita and M. matricarioides. This study presents an evaluation of selected diagnostic characters and anatomical traits of the achene (cypsela) of Matricaria in Turkey using univariate analysis (one-way analysis of variance) and multivariate analysis (cluster analysis, principal component analysis) to obtain new information. Three groups are found within the genus Matricaria based on morphoanatomical characteristics. The colour of disc florets, that of ribs on the achenes, the presence or absence of a slime envelope and pericarp thickness are useful for delimitation of Matricaria taxa, and a key to taxa based on these characters together with other diagnostic traits is provided.

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