scholarly journals Bayesian analysis of censored response data in family-based genetic association studies

2016 ◽  
Vol 58 (5) ◽  
pp. 1039-1053 ◽  
Author(s):  
Fabiola Del Greco M. ◽  
Cristian Pattaro ◽  
Cosetta Minelli ◽  
John R. Thompson
Keyword(s):  
Bayesian Analysis ◽  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Response Data ◽  
Family Based ◽  
Censored Response

scholarly journals Family-Based Samples Can Play an Important Role in Genetic Association Studies

2008 ◽  
Vol 17 (9) ◽  
pp. 2208-2214 ◽  
Author(s):  
Ethan M. Lange ◽  
Jielin Sun ◽  
Leslie A. Lange ◽  
S. Lilly Zheng ◽  
David Duggan ◽  
...  
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Family Based

scholarly journals Accounting for Relatedness in Family Based Genetic Association Studies

2007 ◽  
Vol 64 (4) ◽  
pp. 234-242 ◽  
Author(s):  
P.F. McArdle ◽  
J.R. O’Connell ◽  
T.I. Pollin ◽  
M. Baumgarten ◽  
A.R. Shuldiner ◽  
...  
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Family Based

scholarly journals Genetic association studies: Design, analysis and interpretation

2002 ◽  
Vol 3 (2) ◽  
pp. 146-153 ◽  
Author(s):  
Cathryn M. Lewis
Keyword(s):  
Genetic Association ◽  
Transmission Disequilibrium Test ◽  
Population Stratification ◽  
Genetic Model ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Case Control ◽  
Case Control Studies ◽  
Transmission Disequilibrium ◽  
Family Based

Abstract This paper provides a review of the design and analysis of genetic association studies. In case control studies, the different contingency tables and their relationships to the underlying genetic model are defined. Population stratification is discussed, with suggested methods to identify and correct for the effect. The transmission disequilibrium test is provided as an alternative family-based test, which is robust to population stratification. The relative benefits of each analysis are summarised.

scholarly journals Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies

2021 ◽  
Author(s):  
Debashree Ray ◽  
Candelaria I Vergara ◽  
Margaret I Taub ◽  
Genevieve L Wojcik ◽  
Christine Ladd-Acosta ◽  
...  
Keyword(s):  
Genetic Association ◽  
Statistical Methods ◽  
Population Stratification ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Type I ◽  
Simulation Experiments ◽  
Case Mother ◽  
Family Based ◽  
Parent Child

Genetic association studies of child health outcomes often employ family-based designs. One of the most popular family-based designs is the case-parent trio design that considers the smallest possible nuclear family consisting of two parents and their affected child. This trio design is particularly advantageous for studying relatively rare disorders because it is less prone to type 1 error inflation due to population stratification compared to population-based study designs (e.g., case-control studies). However, obtaining genetic data from both parents is difficult, from a practical perspective, and many large studies predominantly measure genetic variants in mother-child dyads. While some statistical methods for analyzing parent-child dyad data (most commonly involving mother-child pairs) exist, it is not clear if they provide the same advantage as trio methods in protecting against population stratification, or if a specific dyad design (e.g., case-mother dyads vs. case-mother/control-mother dyads) is more advantageous. In this article, we review existing statistical methods for analyzing genome-wide data on dyads and perform extensive simulation experiments to benchmark their type I errors and statistical power under different scenarios. We extend our evaluation to existing methods for analyzing a combination of case-parent trios and dyads together. We apply these methods on genotyped and imputed data from multi-ethnic mother-child pairs only, case-parent trios only or combinations of both dyads and trios from the Gene, Environment Association Studies consortium (GENEVA), where each family was ascertained through a child affected by nonsyndromic cleft lip with or without cleft palate. Results from the GENEVA study corroborate the findings from our simulation experiments. Finally, we provide recommendations for using statistical genetic association methods for dyads.

scholarly journals A Bayesian approach to genetic association studies with family-based designs

2010 ◽  
Vol 34 (6) ◽  
pp. 569-574 ◽  
Author(s):  
Melissa G. Naylor ◽  
Scott T. Weiss ◽  
Christoph Lange
Keyword(s):  
Genetic Association ◽  
Bayesian Approach ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Family Based

scholarly journals Case–Parent Trio Studies in Cleft Lip and Palate

2020 ◽  
Vol 07 (03) ◽  
pp. 075-079
Author(s):  
Mahamad Irfanulla Khan ◽  
Prashanth CS
Keyword(s):  
Genetic Variants ◽  
Cleft Lip ◽  
Cleft Lip And Palate ◽  
Association Studies ◽  
Geographical Location ◽  
Genetic Association Studies ◽  
Population Based ◽  
Genome Wide Association Studies ◽  
Family Based ◽  
Study Designs

AbstractCleft lip with or without cleft palate (CL/P) is one of the most common congenital malformations in humans involving various genetic and environmental risk factors. The prevalence of CL/P varies according to geographical location, ethnicity, race, gender, and socioeconomic status, affecting approximately 1 in 800 live births worldwide. Genetic studies aim to understand the mechanisms contributory to a phenotype by measuring the association between genetic variants and also between genetic variants and phenotype population. Genome-wide association studies are standard tools used to discover genetic loci related to a trait of interest. Genetic association studies are generally divided into two main design types: population-based studies and family-based studies. The epidemiological population-based studies comprise unrelated individuals that directly compare the frequency of genetic variants between (usually independent) cases and controls. The alternative to population-based studies (case–control designs) includes various family-based study designs that comprise related individuals. An example of such a study is a case–parent trio design study, which is commonly employed in genetics to identify the variants underlying complex human disease where transmission of alleles from parents to offspring is studied. This article describes the fundamentals of case–parent trio study, trio design and its significances, statistical methods, and limitations of the trio studies.

scholarly journals Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin K. Esoh ◽  
Tobias O. Apinjoh ◽  
Steven G. Nyanjom ◽  
Ambroise Wonkam ◽  
Emile R. Chimusa ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ethnic Groups ◽  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Genomic Region ◽  
Sub Saharan Africa ◽  
Genome Wide Association Studies ◽  
Fine Scale ◽  
Sub Saharan

AbstractInferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

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