Methods to estimate genetic components of variance for quantitative traits in family studies

Andrade, Mariza de; Amos, Christopher I.; Thiel, T. J.

doi:10.1002/(sici)1098-2272(1999)17:1<64::aid-gepi5>3.0.co;2-m

Cited by 49 publications

(23 citation statements)

References 27 publications

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“…For instance, simulated data adapted from multic R package [2] include 1200 individuals in 200 families, two traits trait1 and trait2 and two covariates age and sex, 6 identity by descent (IBD) multipoint matrices for Chromosomes 5. A smaller subset of 174 individuals in 29 families is available as dat30 data set.…”

Section: Reproducible Examplessupporting

confidence: 91%

solarius: an R interface to SOLAR for variance component analysis in pedigrees

Ziyatdinov

Brunel

Martinez-Perez

et al. 2015

Preprint

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Summary: The open source environment R is one of the most widely used software for statistical computing. It provides a variety of applications including statistical genetics. Most of the powerful tools for quantitative genetic analyses are stand-alone free programs developed by researchers in academia. SOLAR is the standard software program to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. solarius allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. Availability and implementation:solarius is available on CRAN https://cran.r-project.org/package=solarius and on GitHub https://github.com/ugcd/solarius. See http://solar.txbiomedgenetics.org/ for more information about SOLAR.

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Section: Reproducible Examplessupporting

confidence: 91%

solarius: an R interface to SOLAR for variance component analysis in pedigrees

Ziyatdinov

Brunel

Martinez-Perez

et al. 2015

Preprint

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“…We used a polygenic mixed model, a well-known methodology for calculating heritability estimates in family studies (de Andrade, Amos et al, 1999).. Here, it was used to quantify the effect of covariates of MEQ score.…”

Section: Methodsmentioning

confidence: 99%

Amerindian (but not African or European) ancestry is significantly associated with diurnal preference within an admixed Brazilian population

Egan

Santos

Beijamini

et al. 2017

Chronobiology International

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Significant questions remain unanswered regarding the genetic versus environmental contributions to racial/ethnic differences in sleep and circadian rhythms. We addressed this question by investigating the association between diurnal preference, using the Morningness-Eveningness questionnaire (MEQ), and genetic ancestry within the Baependi Heart Study cohort, a highly admixed Brazilian population based in a rural town. Analysis was performed using measures of ancestry, using the Admixture program, and MEQ from 1,453 individuals. We found an association between the degree of Amerindian (but not European of African) ancestry and morningness, equating to 0.16 units for each additional percent of Amerindian ancestry, after adjustment for age, sex, education, and residential zone. To our knowledge, this is the first published report identifying an association between genetic ancestry and MEQ, and above all, the first one based on ancestral contributions within individuals living in the same community. This previously unknown ancestral dimension of diurnal preference suggests a stratification between racial/ethnic groups in an as yet unknown number of genetic polymorphisms.

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“…The overall phenotypic variance was estimated from the observed distribution of trait values in the sample, and was partitioned into genetic and environmental components using the observed covariance among family members, as V 5 2W s 2 a 1 Is 2 e , where V is an nxn matrix of the n individuals in the data set, 2W is the structuring matrix of the coefficient of relationship, and I is an identity matrix that represents the structuring matrix for s 2 e , the variance due to residual environmental factors. Estimates of the mean and variance components were obtained using maximum likelihood methods [47][48][49] . In a practical way, the heritability measures the level of correspondence between the phenotype and its genetic component.…”

Section: Methodsmentioning

confidence: 99%

Distribution and heritability of diurnal preference (chronotype) in a rural Brazilian family-based cohort, the Baependi study

et al. 2015

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Diurnal preference (chronotype) is a useful instrument for studying circadian biology in humans. It harbours trait-like dimensions relating to circadian period and sleep homeostasis, but also has ontogenetic components (morningness increases with age). We used the Morningness-Eveningness questionnaire (MEQ) in the Baependi study, a family-based cohort study based in a small town in Minas Gerais, Brazil. The population is highly admixed and has a cohesive and conservative lifestyle. 825 individuals (497 female) aged 18-89 years (average 6 SD 5 46.4 6 16.3) and belonging to 112 different families participated in this study. The average MEQ score was 63.5 6 11.2 with a significant (P , 0.0001) linear increase with age. Morningness was significantly (P , 0.0001) higher in the rural (70.2 6 9.8) than in the municipal zone (62.6 6 11.1), and was also significantly (P 5 0.025) higher in male (64.6 6 10.9) than in female (62.8 6 11.2) participants. Thus, in spite of universal access to electricity, the Baependi population was strongly shifted towards morningness, particularly in the rural zone. Heritability of MEQ score was 0.48 when adjusted for sex and age, or 0.38 when adjusted for sex, age, and residential zone. The reported MEQ score heritability is more akin to those of previous twin studies than previous family studies.C ircadian period is viewed as a stable and reproducible quantitative trait in humans 1 . It has been found to have a high degree of heritability in all vertebrates where it has been studied 2-4 , and super-short periods have been shown to co-segregate with single-gene mutations both in humans 5 and in model animals 6 . Whilst circadian period may be determined experimentally in humans, most feasibly through the forced desynchrony protocol 7 , it is costly, intrusive, and time-consuming, and thus not a feasible option for large-scale human phenotyping. A more practical proxy for such studies is diurnal preference or chronotype, a self-reported questionnaire-based instrument that yields a numerical score on a scale ranging between extreme morning preference and extreme evening preference. It has been shown to correlate significantly not only with circadian phase, but also with circadian period 8 . However, the trait-like dimension of diurnal preference/chronotype is more complex, as in some individuals, morning versus evening preference results from differences in the build-up or dissipation of homeostatic sleep pressure rather than in circadian parameters [9][10][11] .In addition to its endophenotypic qualities, chronotype is also influenced by state-like variables, some of them of considerable interest to our understanding of the interaction between the circadian oscillator and the sleep homeostat and our external environment 12 . There is a firmly established relationship between chronotype and age, with a peak in eveningness in late adolescence 13 followed by a gradual increase in morningness 14 reflecting an altered relationship between the circadian system and sleep-wake timing 8 .The Morningn...

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Methods to estimate genetic components of variance for quantitative traits in family studies

Cited by 49 publications

References 27 publications

solarius: an R interface to SOLAR for variance component analysis in pedigrees

solarius: an R interface to SOLAR for variance component analysis in pedigrees

Amerindian (but not African or European) ancestry is significantly associated with diurnal preference within an admixed Brazilian population

Distribution and heritability of diurnal preference (chronotype) in a rural Brazilian family-based cohort, the Baependi study

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