Issues in Association Analysis: Error Control in Case-Control Association Studies for Disease Gene Discovery

2004 ◽  
Vol 58 (3-4) ◽  
pp. 171-174 ◽  
Author(s):  
Jurg Ott
Keyword(s):  
Association Analysis ◽  
Error Control ◽  
Disease Gene ◽  
Association Studies ◽  
Gene Discovery ◽  
Case Control ◽  
Disease Gene Discovery ◽  
Analysis Error ◽  
Control Association

scholarly journals GRIPT: A novel case-control analysis method for Mendelian disease gene discovery

2018 ◽  
Author(s):  
Jun Wang ◽  
Li Zhao ◽  
Xia Wang ◽  
Yong Chen ◽  
Mingchu Xu ◽  
...  
Keyword(s):  
Disease Gene ◽  
Gene Discovery ◽  
Case Control ◽  
Mendelian Disease ◽  
Control Analysis ◽  
Mendelian Diseases ◽  
Disease Gene Discovery ◽  
Main Challenge ◽  
Case Control Analysis ◽  
Ngs Data

AbstractDespite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about 50% of Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity.

scholarly journals GRIPT: a novel case-control analysis method for Mendelian disease gene discovery

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Jun Wang ◽  
Li Zhao ◽  
Xia Wang ◽  
Yong Chen ◽  
Mingchu Xu ◽  
...  
Keyword(s):  
Disease Gene ◽  
Gene Discovery ◽  
Case Control ◽  
Mendelian Disease ◽  
Control Analysis ◽  
Analysis Method ◽  
Disease Gene Discovery ◽  
Case Control Analysis

scholarly journals First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery

2020 ◽  
Vol 28 (8) ◽  
pp. 1034-1043 ◽  
Author(s):  
Holger Hengel ◽  
Rebecca Buchert ◽  
Marc Sturm ◽  
Tobias B. Haack ◽  
Yvonne Schelling ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Neurological Disorders ◽  
Disease Gene ◽  
Gene Discovery ◽  
First Line ◽  
Disease Gene Discovery ◽  
Israeli Arabs

scholarly journals Disease Modeling and Disease Gene Discovery in Cardiomyopathies: A Molecular Study of Induced Pluripotent Stem Cell Generated Cardiomyocytes

2021 ◽  
Vol 22 (7) ◽  
pp. 3311
Author(s):  
Satish Kumar ◽  
Joanne E. Curran ◽  
Kashish Kumar ◽  
Erica DeLeon ◽  
Ana C. Leandro ◽  
...  
Keyword(s):  
Stem Cell ◽  
Pluripotent Stem Cell ◽  
Disease Gene ◽  
Disease Modeling ◽  
Gene Discovery ◽  
Induced Pluripotent Stem Cell ◽  
P Value ◽  
Disease Gene Discovery ◽  
Induced Pluripotent

The in vitro modeling of cardiac development and cardiomyopathies in human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (CMs) provides opportunities to aid the discovery of genetic, molecular, and developmental changes that are causal to, or influence, cardiomyopathies and related diseases. To better understand the functional and disease modeling potential of iPSC-differentiated CMs and to provide a proof of principle for large, epidemiological-scale disease gene discovery approaches into cardiomyopathies, well-characterized CMs, generated from validated iPSCs of 12 individuals who belong to four sibships, and one of whom reported a major adverse cardiac event (MACE), were analyzed by genome-wide mRNA sequencing. The generated CMs expressed CM-specific genes and were highly concordant in their total expressed transcriptome across the 12 samples (correlation coefficient at 95% CI =0.92 ± 0.02). The functional annotation and enrichment analysis of the 2116 genes that were significantly upregulated in CMs suggest that generated CMs have a transcriptomic and functional profile of immature atrial-like CMs; however, the CMs-upregulated transcriptome also showed high overlap and significant enrichment in primary cardiomyocyte (p-value = 4.36 × 10−9), primary heart tissue (p-value = 1.37 × 10−41) and cardiomyopathy (p-value = 1.13 × 10−21) associated gene sets. Modeling the effect of MACE in the generated CMs-upregulated transcriptome identified gene expression phenotypes consistent with the predisposition of the MACE-affected sibship to arrhythmia, prothrombotic, and atherosclerosis risk.

scholarly journals Leveraging Family History in Population-Based Case-Control Association Studies

2014 ◽  
Vol 38 (2) ◽  
pp. 114-122 ◽  
Author(s):  
Arpita Ghosh ◽  
Patricia Hartge ◽  
Peter Kraft ◽  
Amit D. Joshi ◽  
Regina G. Ziegler ◽  
...  
Keyword(s):  
Family History ◽  
Association Studies ◽  
Population Based ◽  
Case Control ◽  
Control Association

A Retrospective Likelihood Approach for Efficient Integration of Multiple Omics Factors in Case-Control Association Studies

2015 ◽  
Vol 39 (3) ◽  
pp. 156-165 ◽  
Author(s):  
Brunilda Balliu ◽  
Roula Tsonaka ◽  
Stefan Boehringer ◽  
Jeanine Houwing-Duistermaat
Keyword(s):  
Association Studies ◽  
Case Control ◽  
Efficient Integration ◽  
Retrospective Likelihood ◽  
Likelihood Approach ◽  
Control Association
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