The Impact of Phenocopy on the Genetic Analysis of Complex Traits

AbstractUnemployment shocks from the COVID-19 pandemic have reignited concerns over the long-term effects of job loss on population health. Past research has highlighted the corrosive effects of unemployment on health and health behaviors. This study examines whether the effects of job loss on changes in body mass index (BMI) are moderated by genetic predisposition using data from the U.S. Health and Retirement Study (HRS). To improve detection of gene-by-environment (G × E) interplay, we interacted layoffs from business closures—a plausibly exogenous environmental exposure—with whole-genome polygenic scores (PGSs) that capture genetic contributions to both the population mean (mPGS) and variance (vPGS) of BMI. Results show evidence of genetic moderation using a vPGS (as opposed to an mPGS) and indicate genome-wide summary measures of phenotypic plasticity may further our understanding of how environmental stimuli modify the distribution of complex traits in a population.

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Genetic analysis of Ghanaian G1P[8] and G9P[8] rotavirus A strains reveals the impact of P[8] VP4 gene polymorphism on P-genotyping

PLoS ONE ◽

10.1371/journal.pone.0218790 ◽

2019 ◽

Vol 14 (6) ◽

pp. e0218790 ◽

Cited By ~ 6

Author(s):

Susan Afua Damanka ◽

Chantal Ama Agbemabiese ◽

Francis Ekow Dennis ◽

Belinda Larteley Lartey ◽

Theophilus Korku Adiku ◽

...

Keyword(s):

Genetic Analysis ◽

Gene Polymorphism ◽

Rotavirus A ◽

The Impact

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Genetic analysis of complex traits using clonal rainbow trout lines

Aquatic Genomics ◽

10.1007/978-4-431-65938-9_35 ◽

2003 ◽

pp. 395-398 ◽

Cited By ~ 1

Author(s):

Gary H. Thorgaard ◽

Paul A. Wheeler ◽

William P. Young ◽

Barrie D. Robison ◽

Sandra S. Ristow

Keyword(s):

Rainbow Trout ◽

Genetic Analysis ◽

Complex Traits

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Genetic analysis of complex traits via Bayesian variable selection: the utility of a mixture of uniform priors

Genetics Research ◽

10.1017/s0016672311000164 ◽

2011 ◽

Vol 93 (4) ◽

pp. 303-318 ◽

Cited By ~ 12

Author(s):

TIMO KNÜRR ◽

ESA LÄÄRÄ ◽

MIKKO J. SILLANPÄÄ

Keyword(s):

Genetic Analysis ◽

Variable Selection ◽

Complex Traits ◽

Bayesian Variable Selection ◽

Stochastic Search Variable Selection ◽

Indicator Variables ◽

Supplementary Material ◽

Selection Of ◽

Made In ◽

Search Variable

SummaryA new estimation-based Bayesian variable selection approach is presented for genetic analysis of complex traits based on linear or logistic regression. By assigning a mixture of uniform priors (MU) to genetic effects, the approach provides an intuitive way of specifying hyperparameters controlling the selection of multiple influential loci. It aims at avoiding the difficulty of interpreting assumptions made in the specifications of priors. The method is compared in two real datasets with two other approaches, stochastic search variable selection (SSVS) and a re-formulation of Bayes B utilizing indicator variables and adaptive Student's t-distributions (IAt). The Markov Chain Monte Carlo (MCMC) sampling performance of the three methods is evaluated using the publicly available software OpenBUGS (model scripts are provided in the Supplementary material). The sensitivity of MU to the specification of hyperparameters is assessed in one of the data examples.

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Second reply to the comment by Romero and Kannada on “Genetic analysis of 16th-century whale bones prompts a revision of the impact of Basque whaling on right and bowhead whales in the western North Atlantic”Appears in Can. J. Zool. 84(7): 1059–1065.

Canadian Journal of Zoology ◽

10.1139/z07-118 ◽

2008 ◽

Vol 86 (1) ◽

pp. 76-79 ◽

Cited By ~ 1

Author(s):

Jeff W. Higdon

Keyword(s):

Genetic Analysis ◽

North Atlantic ◽

16Th Century ◽

Bowhead Whales ◽

Potential Value ◽

The North ◽

The Pacific ◽

History Of ◽

The North Atlantic ◽

The Impact

The comments by A. Romero and S. Kannada (2006. Can. J. Zool. 84: 1059–1065) provide a brief summary of North Atlantic whaling history as a critique of T. Rastogi et al. (2004. Can. J. Zool. 82: 1647–1654) . However, they fall far short of providing an accurate review of whaling history in this region. The authors present a number of factual errors, misuse several key sources, and make significant omissions, ultimately defeating the purpose of providing information to biologists, managers, and historians. In this comment I highlight the mistakes in their representation of the history of North Atlantic whaling for bowhead whales ( Balaena mysticetus L., 1758). There are unacceptable errors for most nations covered, and for American whaling in particular. The authors assert that over 30 000 bowhead whales were landed by Yankee whalers in the North Atlantic when the vast majority were in fact taken on the Pacific grounds. Although a summary of whaling history is an admirable goal and of potential value, it is unfortunate that the authors missed such an opportunity by failing to adequately research this topic, failing to include important citations, and by including sources that do not provide the information indicated. Providing a whaling summary with such errors and omissions only adds further confusion to an already confusing theme.

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The association between the serotonin and dopamine neurotransmitters and personality traits

Epidemiology and Psychiatric Sciences ◽

10.1017/s2045796015001146 ◽

2016 ◽

Vol 25 (2) ◽

pp. 109-112 ◽

Cited By ~ 5

Author(s):

G. Delvecchio ◽

M. Bellani ◽

A. C. Altamura ◽

P. Brambilla

Keyword(s):

Personality Traits ◽

Psychiatric Disorders ◽

Candidate Genes ◽

Genetic Polymorphisms ◽

Complex Traits ◽

Healthy Subjects ◽

Mental Illnesses ◽

Biological Mechanisms ◽

Normal Personality ◽

The Impact

Evidence from previous studies has reported that complex traits, including psychiatric disorders, are moderately to highly heritable. Moreover, it has also been shown that specific personality traits may increase the risk to develop mental illnesses. Therefore the focus of the research shifted towards the identification of the biological mechanisms underpinning these traits by exploring the effects of a constellation of genetic polymorphisms in healthy subjects. Indeed, studying the effect of genetic variants in normal personality provides a unique means for identifying candidate genes which may increase the risk for psychiatric disorders. In this review, we discuss the impact of two of the most frequently studied genetic polymorphisms on personality in healthy subjects, the 5-HTT polymorphism of the serotonin transporter and the DRD2/DRD4 polymorphisms of the D2/D4 dopamine's receptors. The main aims are: (a) to highlight that the study of candidate genes provides a fruitful ground for the identification of the biological underpinnings of personality without, though, reaching a general consensus about the strength of this relationship; and (b) to outline that the research in personality genetics should be expanded to provide a clearer picture of the heritability of personality traits.

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The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material

Biology ◽

10.3390/biology9080229 ◽

2020 ◽

Vol 9 (8) ◽

pp. 229 ◽

Cited By ~ 1

Author(s):

Andrea Arrones ◽

Santiago Vilanova ◽

Mariola Plazas ◽

Giulio Mangino ◽

Laura Pascual ◽

...

Keyword(s):

Genetic Analysis ◽

Plant Breeding ◽

Complex Traits ◽

Genetic Recombination ◽

Phenotypic Diversity ◽

Recombinant Inbred Lines ◽

Plant Genetic Resources ◽

Diallel Cross ◽

Genetic Mosaic ◽

Selection Of

The compelling need to increase global agricultural production requires new breeding approaches that facilitate exploiting the diversity available in the plant genetic resources. Multi-parent advanced generation inter-cross (MAGIC) populations are large sets of recombinant inbred lines (RILs) that are a genetic mosaic of multiple founder parents. MAGIC populations display emerging features over experimental bi-parental and germplasm populations in combining significant levels of genetic recombination, a lack of genetic structure, and high genetic and phenotypic diversity. The development of MAGIC populations can be performed using “funnel” or “diallel” cross-designs, which are of great relevance choosing appropriate parents and defining optimal population sizes. Significant advances in specific software development are facilitating the genetic analysis of the complex genetic constitutions of MAGIC populations. Despite the complexity and the resources required in their development, due to their potential and interest for breeding, the number of MAGIC populations available and under development is continuously growing, with 45 MAGIC populations in different crops being reported here. Though cereals are by far the crop group where more MAGIC populations have been developed, MAGIC populations have also started to become available in other crop groups. The results obtained so far demonstrate that MAGIC populations are a very powerful tool for the dissection of complex traits, as well as a resource for the selection of recombinant elite breeding material and cultivars. In addition, some new MAGIC approaches that can make significant contributions to breeding, such as the development of inter-specific MAGIC populations, the development of MAGIC-like populations in crops where pure lines are not available, and the establishment of strategies for the straightforward incorporation of MAGIC materials in breeding pipelines, have barely been explored. The evidence that is already available indicates that MAGIC populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of dramatically improved cultivars.

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