Recent genomic heritage in Scotland

Amador, Carmen; Huffman, Jennifer E.; Trochet, Holly; Campbell, Archie; Porteous, David J.; Wilson, James F.; Hastie, Nick; Vitart, Véronique; Hayward, Caroline; Navarro, Pau; Haley, Chris

doi:10.1186/s12864-015-1605-2

Cited by 53 publications

(55 citation statements)

References 30 publications

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“…Details of genotyping are described elsewhere (Smith et al, 2006). Population outlier individuals were removed from the sample (Amador et al, 2015). Quality control (QC) of genotyped SNPs used inclusion thresholds: missing SNPs per individual ≤ 2%, SNP genotype call rate ≥ 98%, minor allele frequency (MAF) > 1% and Hardy-Weinberg equilibrium P value > 1 × 10 − 6 .…”

Section: Methodsmentioning

confidence: 99%

Shared Genetics and Couple-Associated Environment Are Major Contributors to the Risk of Both Clinical and Self-Declared Depression

et al. 2016

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BackgroundBoth genetic and environmental factors contribute to risk of depression, but estimates of their relative contributions are limited. Commonalities between clinically-assessed major depressive disorder (MDD) and self-declared depression (SDD) are also unclear.MethodsUsing data from a large Scottish family-based cohort (GS:SFHS, N = 19,994), we estimated the genetic and environmental variance components for MDD and SDD. The components representing the genetic effect associated with genome-wide common genetic variants (SNP heritability), the additional pedigree-associated genetic effect and non-genetic effects associated with common environments were estimated in a linear mixed model (LMM).FindingsBoth MDD and SDD had significant contributions from components representing the effect from common genetic variants, the additional genetic effect associated with the pedigree and the common environmental effect shared by couples. The estimate of correlation between SDD and MDD was high (r = 1.00, se = 0.20) for common-variant-associated genetic effect and lower for the additional genetic effect from the pedigree (r = 0.57, se = 0.08) and the couple-shared environmental effect (r = 0.53, se = 0.22).InterpretationBoth genetics and couple-shared environmental effects were major factors influencing liability to depression. SDD may provide a scalable alternative to MDD in studies seeking to identify common risk variants. Rarer variants and environmental effects may however differ substantially according to different definitions of depression.

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Section: Methodsmentioning

confidence: 99%

Shared Genetics and Couple-Associated Environment Are Major Contributors to the Risk of Both Clinical and Self-Declared Depression

et al. 2016

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“…Each phenotype was then regressed on age, sex, and 10 genetic principal components [25] with the residuals being entered as the dependent variable in the LASSO models.…”

Section: Phenotype Preparation In Generation Scotlandmentioning

confidence: 99%

Epigenetic prediction of complex traits and death

McCartney

Stevenson

Ritchie

et al. 2018

Preprint

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Word Count (abstract): 241Word Count (body): 3,696 . CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/294116 doi: bioRxiv preprint first posted online Apr. 3, 2018; was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. List of abbreviationsThe copyright holder for this preprint (which . http://dx.doi.org/10.1101/294116 doi: bioRxiv preprint first posted online Apr. 3, 2018; Abstract:Background:

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“…The subsequent dataset was combined with the 1,092 individuals of the 1000 Genomes population (52) before principal components being calculated in GCTA (53). Outliers, defined by being more than 6 SDs away from the mean of the first two principal components, were removed (54). This left a sample of 20,032 participants.…”

Section: Methodsmentioning

confidence: 99%

Genetic variants linked to education predict longevity

Marioni¹,

Ritchie²,

Joshi³

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Educational attainment is associated with many health outcomes, including longevity. It is also known to be substantially heritable. Here, we used data from three large genetic epidemiology cohort studies (Generation Scotland, n = ∼17,000; UK Biobank, n = ∼115,000; and the Estonian Biobank, n = ∼6,000) to test whether education-linked genetic variants can predict lifespan length. We did so by using cohort members' polygenic profile score for education to predict their parents' longevity. Across the three cohorts, meta-analysis showed that a 1 SD higher polygenic education score was associated with ∼2.7% lower mortality risk for both mothers (total n deaths = 79,702) and ∼2.4% lower risk for fathers (total n deaths = 97,630). On average, the parents of offspring in the upper third of the polygenic score distribution lived 0.55 y longer compared with those of offspring in the lower third. Overall, these results indicate that the genetic contributions to educational attainment are useful in the prediction of human longevity.genetics | education | longevity | prediction | polygenic score

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Recent genomic heritage in Scotland

Cited by 53 publications

References 30 publications

Shared Genetics and Couple-Associated Environment Are Major Contributors to the Risk of Both Clinical and Self-Declared Depression

Shared Genetics and Couple-Associated Environment Are Major Contributors to the Risk of Both Clinical and Self-Declared Depression

Epigenetic prediction of complex traits and death

Genetic variants linked to education predict longevity

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