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Human Heredity

Wei Vivian Zhuang, Joanne M Murabito, Kathryn L Lunetta
BACKGROUND: In longitudinal epidemiological studies there may be individuals with rich phenotype data who die or are lost to follow-up before providing DNA for genetic studies. Often, the genotypic and phenotypic data of the relatives are available. Two strategies for analyzing the incomplete data are to exclude ungenotyped subjects from analysis (the complete-case method, CC) and to include phenotyped but ungenotyped individuals in analysis by using relatives' genotypes for genotype imputation (GI)...
August 31, 2016: Human Heredity
Emily Slade, Peter Kraft
OBJECTIVE: The association between DNA methylation and a trait of interest may depend on an environmental exposure, and incorrectly accounting for this dependence can lead to a reduction in power of the standard tests used in epigenome-wide association studies. We present the M-ME test to jointly test for the main effect of DNA methylation and methylation-environment interaction. METHODS: Through simulation, we compare the power and type 1 error of the M-ME test to a standard marginal test (M test) and a standard interaction test (ME test) under 1,800 different underlying models...
August 5, 2016: Human Heredity
Alexandre Bureau, Jordie Croteau
OBJECTIVES: To investigate the conditions and analysis strategies required so that endophenotypes related to a disease help discover genetic variants involved in the disease. METHODS: The association with disease susceptibility variants is examined as a function of the relationships between disease status, endophenotype values and the genotype at another disease or endophenotype susceptibility locus assumed to be previously known, using approximate linear models of allele frequencies as a function of these variables and simulations in the context of family studies when the endophenotype is dichotomous...
July 30, 2016: Human Heredity
Stacey Knight, Arthur T Maness, Sue M Dintelman, Benjamin D Horne
BACKGROUND: Many landmark genetic breakthroughs, including the recent discovery of PCSK-9 inhibitor drugs, were accomplished with substantial contributions from evaluation of pedigrees. Finding and ascertaining high-value pedigrees is not trivial and requires considerable time and cost. Here, we describe the creation of the Intermountain Genealogy Registry for use in studying the genetics of cardiovascular and other diseases. METHODS: Using publicly available pedigree records and probabilistic linkage techniques, we created a genealogy of ≈23 million records that we linked to 3...
July 16, 2016: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
March 11, 2015: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
2015: Human Heredity
Claire Dandine-Roulland, Hervé Perdry
We give a short but detailed review of the methods used to deal with linear mixed models (restricted likelihood, AIREML algorithm, best linear unbiased predictors, etc.), with a few original points. Then we describe three common applications of the linear mixed model in contemporary human genetics: association testing (pathways analysis or rare variants association tests), genomic heritability estimates, and correction for population stratification in genome-wide association studies. We also consider the performance of best linear unbiased predictors for prediction in this context, through a simulation study for rare variants in a short genomic region, and through a short theoretical development for genome-wide data...
2015: Human Heredity
Duo Jiang, Joelle Mbatchou, Mary Sara McPeek
Case-control genetic association analysis is an extremely common tool in human complex trait mapping. From a statistical point of view, the analysis of binary traits poses somewhat different challenges from the analysis of quantitative traits. Desirable features of a binary trait mapping approach would include (1) phenotype modeled as binary, with appropriate dependence between the mean and variance; (2) appropriate correction for relevant covariates; (3) appropriate correction for sample structure of various types, including related individuals, admixture and other types of population structure; (4) both fast and accurate computations; (5) robustness to ascertainment and other types of phenotype model misspecification, and (6) ability to leverage partially missing data to increase power...
2015: Human Heredity
Frank Dudbridge, Paul J Newcombe
OBJECTIVE: Gene scores are often used to model the combined effects of genetic variants. When variants are in linkage disequilibrium, it is common to prune all variants except the most strongly associated. This avoids duplicating information but discards information when variants have independent effects. However, joint modelling of correlated variants increases the sampling error in the gene score. In recent applications, joint modelling has offered only small improvements in accuracy over pruning...
2015: Human Heredity
Emmanuelle Génin, Françoise Clerget-Darpoux
Most studies on multifactorial diseases are performed under the assumption of a polygenic additive liability. In particular, missing heritability and individual risk scores are estimated under this model. In this paper, we use the example of diabetes to highlight the pitfalls of relying on such a model, when there are reasons to suspect etiological heterogeneity and/or departure from the hypotheses on the environmental factor effects.
2015: Human Heredity
Peter M Visscher, Naomi R Wray
It is nearly one hundred years, since R.A. Fisher published his now famous paper that started the field of quantitative genetics. That paper reconciled Mendelian genetics (as exemplified by Mendel's peas) and the biometrical approach to quantitative traits (as exemplified by the correlation and regression approaches from Galton and Pearson), by showing that a simple model of many genes of small effects, each following Mendel's laws of segregation and inheritance, plus environmental variation could account for the observed resemblance between relatives...
2015: Human Heredity
Jurg Ott
After a brief discussion and evaluation of Fisher's additive polygenic inheritance model, a few other approaches to polygenic inheritance are discussed, notably the polygenic threshold model. A literature review of applications of such models in human genetics is presented, and a simple approach, based on a finite polygenic model, is developed in detail. The fit of the model to recurrence risks in schizophrenia is discussed.
2015: Human Heredity
John P A Ioannidis
No abstract text is available yet for this article.
2015: Human Heredity
Emmanuelle Génin, Françoise Clerget-Darpoux
No abstract text is available yet for this article.
2015: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
2015: Human Heredity
Huanhuan Zhu, Shuanglin Zhang, Qiuying Sha
BACKGROUND/AIMS: Genome-wide association studies (GWAS) have identified many variants that each affect multiple phenotypes, which suggests that pleiotropic effects on human complex phenotypes may be widespread. Therefore, statistical methods that can jointly analyze multiple phenotypes in GWAS may have advantages over analyzing each phenotype individually. Several statistical methods have been developed to utilize such multivariate phenotypes in genetic association studies; however, the performance of these methods under different scenarios is largely unknown...
2015: Human Heredity
Bárbara Xoana Granata, Victoria Estela Parera, Alcira Batlle, María Victoria Rossetti
BACKGROUND/AIMS: The porphyrias are genetically heterogeneous diseases, and each mutation is exclusive to one or two families. Among the mutations responsible for variegate porphyria in our country, c.1042_1043insT stands out, since it was described only in Argentina and is present in about 40% of genetically diagnosed families. Thus, we hypothesized the possible existence of a common ancestor for the mutation in our population. METHODS: We conducted a study based on microsatellite (short tandem repeats) haplotypes...
2015: Human Heredity
Qi Yan, Daniel E Weeks, Hemant K Tiwari, Nengjun Yi, Kui Zhang, Guimin Gao, Wan-Yu Lin, Xiang-Yang Lou, Wei Chen, Nianjun Liu
OBJECTIVE: The kernel machine (KM) test reportedly performs well in the set-based association test of rare variants. Many studies have been conducted to measure phenotypes at multiple time points, but the standard KM methodology has only been available for phenotypes at a single time point. In addition, family-based designs have been widely used in genetic association studies; therefore, the data analysis method used must appropriately handle familial relatedness. A rare-variant test does not currently exist for longitudinal data from family samples...
2015: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
2015: Human Heredity
Meng Yuan Xu, David M Umbach, Eleanor Murphy, Francis McMahon, Yin Y Shugart
OBJECTIVE: Drugs take effect at different times in different individuals. Consequently, researchers seek to examine how the timing of the biological response to drugs may be affected by factors such as gender, genotypes, age, or baseline symptom scores. METHODS: Typically, studies measure symptoms immediately after the initiation of drug treatment and then at a sequence of later time points. In this study, we develop a statistical mixture model for analyzing such longitudinal data...
2015: Human Heredity
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