scholarly journals An omnibus test for family-based association studies with multiple SNPs and multiple phenotypes

2010 ◽  
Vol 18 (6) ◽  
pp. 720-725 ◽  
Author(s):  
Jessica Lasky-Su ◽  
Amy Murphy ◽  
Matthew B McQueen ◽  
Scott Weiss ◽  
Christoph Lange
Keyword(s):  
Association Studies ◽  
Omnibus Test ◽  
Multiple Snps ◽  
Multiple Phenotypes ◽  
Family Based

A New Powerful Non-Parametric Two-Stage Approach for Testing Multiple Phenotypes in Family-Based Association Studies

2003 ◽  
Vol 56 (1-3) ◽  
pp. 10-17 ◽  
Author(s):  
Christoph Lange ◽  
Helen Lyon ◽  
Dawn DeMeo ◽  
Benjamin Raby ◽  
Edwin K. Silverman ◽  
...  
Keyword(s):  
Association Studies ◽  
Two Stage ◽  
Multiple Phenotypes ◽  
Family Based ◽  
Non Parametric

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 Family-based gene-environment interaction using sequence kernel association test (FGE-SKAT) for complex quantitative traits

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chao-Yu Guo ◽  
Reng-Hong Wang ◽  
Hsin-Chou Yang
Keyword(s):  
Complex Traits ◽  
Association Studies ◽  
Association Test ◽  
Whole Genome Sequence ◽  
Environment Interaction ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Sequence Kernel Association Test ◽  
Gene Environment ◽  
Family Based

AbstractAfter the genome-wide association studies (GWAS) era, whole-genome sequencing is highly engaged in identifying the association of complex traits with rare variations. A score-based variance-component test has been proposed to identify common and rare genetic variants associated with complex traits while quickly adjusting for covariates. Such kernel score statistic allows for familial dependencies and adjusts for random confounding effects. However, the etiology of complex traits may involve the effects of genetic and environmental factors and the complex interactions between genes and the environment. Therefore, in this research, a novel method is proposed to detect gene and gene-environment interactions in a complex family-based association study with various correlated structures. We also developed an R function for the Fast Gene-Environment Sequence Kernel Association Test (FGE-SKAT), which is freely available as supplementary material for easy GWAS implementation to unveil such family-based joint effects. Simulation studies confirmed the validity of the new strategy and the superior statistical power. The FGE-SKAT was applied to the whole genome sequence data provided by Genetic Analysis Workshop 18 (GAW18) and discovered concordant and discordant regions compared to the methods without considering gene by environment interactions.

scholarly journals Genetic Determinants of Paget’s Disease of Bone

2021 ◽  
Author(s):  
Navnit S. Makaram ◽  
Stuart H. Ralston
Keyword(s):  
Genetic Factors ◽  
Association Studies ◽  
Paget’S Disease ◽  
Paget's Disease ◽  
Paget’S Disease Of Bone ◽  
Genome Wide Association Studies ◽  
Paget's Disease Of Bone ◽  
Genome Wide ◽  
Family Based

Abstract Purpose of Review To provide an overview of the role of genes and loci that predispose to Paget’s disease of bone and related disorders. Recent Findings Studies over the past ten years have seen major advances in knowledge on the role of genetic factors in Paget’s disease of bone (PDB). Genome wide association studies have identified six loci that predispose to the disease whereas family based studies have identified a further eight genes that cause PDB. This brings the total number of genes and loci implicated in PDB to fourteen. Emerging evidence has shown that a number of these genes also predispose to multisystem proteinopathy syndromes where PDB is accompanied by neurodegeneration and myopathy due to the accumulation of abnormal protein aggregates, emphasising the importance of defects in autophagy in the pathogenesis of PDB. Summary Genetic factors play a key role in the pathogenesis of PDB and the studies in this area have identified several genes previously not suspected to play a role in bone metabolism. Genetic testing coupled to targeted therapeutic intervention is being explored as a way of halting disease progression and improving outcome before irreversible skeletal damage has occurred.

scholarly journals Implicit Hypotheses Are Hidden Power Droppers in Family-Based Association Studies of Secondary Outcomes

2015 ◽  
Vol 05 (01) ◽  
pp. 35-45 ◽  
Author(s):  
Jean Gaschignard ◽  
Quentin B. Vincent ◽  
Jean-Philippe Jaïs ◽  
Aurélie Cobat ◽  
Alexandre Alcaïs
Keyword(s):  
Association Studies ◽  
Secondary Outcomes ◽  
Family Based

Association of HLA Class II Alleles and Haplotypes with Type 1 Diabetes in Tunisian Arabs

2018 ◽  
Vol 127 (10) ◽  
pp. 653-662
Author(s):  
Abdelhafidh Hajjej ◽  
Wassim Y. Almawi ◽  
Mouna Stayoussef ◽  
Lasmar Hattab ◽  
Slama Hmida
Keyword(s):  
Type 1 Diabetes ◽  
Association Studies ◽  
Class Ii ◽  
Correlation Study ◽  
Case Control ◽  
Linkage Study ◽  
Hla Class Ii ◽  
Racial Background ◽  
Family Based

AbstractThe molecular association of HLA class II with type 1 diabetes (T1DM) was investigated in Tunisian Arabs using 3 kinds of analyses. The first was a case-control association study, using Relative Predispositional Effects method, involved 137 T1DM cases and 258 control subjects. The second was family-based association-linkage study, using Transmission Disequilibrium Test, and covering 50 Tunisian families comprising 73 T1DM patients and 100 parents. The third was a wide correlation study between 4 DRB1 alleles (DRB1*03, *04, *11, *15) and T1DM in 52 countries, using Spearman’s Rho. Results from Case-control and family-based association studies showed that DRB1*03 and DRB1*04 alleles predispose to T1DM in Tunisian Arabs. Conversely, only DRB1*11 was protective for T1DM. DRB1*04-DQB1*03 haplotype was consistently associated positively with T1DM; DRB1*03/DRB1*04 genotype had the highest risk of T1DM development. Compared to DRB1*03, HLA-DRB1*04 was associated with higher T1DM incidence. Thus, the contribution of HLA class II to T1DM genetic susceptibility must be evaluated with regards to specific HLA alleles, genotypes, and haplotypes, and also ethnic and racial background.

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