Statistical methods for multi-marker testing in genetic association studies

2012 ◽  
Author(s):  
Yilin Dai
Keyword(s):  
Genetic Association ◽  
Statistical Methods ◽  
Association Studies ◽  
Genetic Association Studies

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 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.

scholarly journals Evaluation of genome-wide power of genetic association studies based on empirical data from the HapMap project

2007 ◽  
Vol 16 (20) ◽  
pp. 2494-2505 ◽  
Author(s):  
Yasuhito Nannya ◽  
Kenjiro Taura ◽  
Mineo Kurokawa ◽  
Shigeru Chiba ◽  
Seishi Ogawa
Keyword(s):  
Genetic Association ◽  
Empirical Data ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Hapmap Project ◽  
Genome Wide

scholarly journals Clinical, biochemical and genetic risk factors for 30-day and 5-year mortality in 518 adult patients subjected to cardiopulmonary bypass during cardiac surgery - the INFLACOR study.

2018 ◽  
Vol 65 (2) ◽  
pp. 241-250 ◽  
Author(s):  
Maciej Michał Kowalik ◽  
Romuald Lango ◽  
Piotr Siondalski ◽  
Magdalena Chmara ◽  
Maciej Brzeziński ◽  
...  
Keyword(s):  
Risk Factors ◽  
Cardiac Surgery ◽  
Cardiopulmonary Bypass ◽  
Genetic Association ◽  
Biochemical Parameters ◽  
Cox Regression ◽  
Association Studies ◽  
Nyha Class ◽  
Genetic Association Studies ◽  
Chronic Obstructive

There is increasing evidence that genetic variability influence patients’ early morbidity after cardiac surgery performed using cardiopulmonary bypass (CPB). The use of mortality as an outcome measure in cardiac surgical genetic association studies is rare. We publish the 30-day and 5-year survival analyses with focus on pre-, intra-, postoperative variables, biochemical parameters, and genetic variants in the INFLACOR (INFlAmmation in Cardiac OpeRations) cohort.In a series of prospectively recruited 518 adult Polish Caucasians who underwent cardiac surgery in which CPB was used, the clinical data, biochemical parameters, IL-6, soluble ICAM-1, TNFa, soluble E-selectin, and 10 single nucleotide polymorphisms were evaluated for their associations with 30-day and 5-year mortality.The 30-day mortality was associated with: pre-operative prothrombin international normalized ratio, intra-operative blood lactate, postoperative serum creatine phosphokinase, and acute kidney injury requiring renal replacement therapy (AKI-RRT) in logistic regression. Factors that determined the 5-year survival included: pre-operative NYHA class, history of peripheral artery disease and severe chronic obstructive pulmonary disease, intra-operative blood transfusion; and postoperative peripheral hypothermia, myocardial infarction, infection, and AKI-RRT in Cox regression. The serum levels of IL-6 and ICAM-1 measured three hours after operation were associated with 30-day and 5-year mortality, respectively. The ICAM1 rs5498 was associated with 30-day and 5-year survival with borderline significance.Different risk factors determined the early (30-day) and late (5-year) survival after adult cardiac surgery in which cardiopulmonary bypass was used. Future genetic association studies in cardiac surgical patients should adjust for the identified chronic and acute postoperative risk factors.

scholarly journals The value of some Corsican sub-populations for genetic association studies

2008 ◽  
Vol 9 (1) ◽  
Author(s):  
Veronica Latini ◽  
Gabriella Sole ◽  
Laurent Varesi ◽  
Giuseppe Vona ◽  
Maria Serafina Ristaldi
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies
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