Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood

By Sang Hong Lee, Jian Yang, Michael E. Goddard, Peter M. Visscher, Naomi R. Wray. Bioinform., 2012

647 citations recorded by the source corpus.

Subfields: Genetics, Health, Toxicology and Mutagenesis

View Paper: https://www.semanticscholar.org/paper/1657ab17a5b554422360ea8fb2b4aaffa6ec5d2d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Health, Toxicology and Mutagenesis

Citations in the corpus

Genetics and Intelligence Differences: Five Special Findings (2014, positive): “The value of GCTA has been greatly increased by extending it beyond the univariate analysis of the variance of a single trait to the bivariate analysis of the covariance between two traits or the ‘same’ trait at two ages 44, 45 ; a recent approach is multivariate rather than just bivariate 46 .”
An Atlas of Genetic Correlations across Human Diseases and Traits (2015, background): “Precisely, under a polygenic model [13,15], the expected value of where N i is the sample size for study i , ρ g is genetic covariance (deﬁned in Methods), (cid:96) j is LD Score [21], N s is the number of individuals included in both studies, and ρ is the phenotypic correlation among the N s…”
ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social-communication difficulties (2017, neutral): “Genome-wide Complex Trait Analysis (GCTA)49,50 was utilised to estimate SNP-h 2 and genetic correlations among SCDC scores, as published previously27, for comparison only (Supplementary methods).”
Efficient Algorithms for Multivariate Linear Mixed Models in Genome-wide Association Studies (2013, methodology): “ hand, the NR algorithm is fast to converge given a good initial value (only takes a few iterations), but can easily fail to do so given a bad starting point. Therefore, we follow previous approaches [31, 32, 30, 29, 4] and combine the two algorithms together, with the PX-EM algorithm providing a go”
Genome-wide association study identifies 74 loci associated with educational attainment (2016, methodology): “(7) Fst = 2 N [n1 (p1 − ?̅?) 2 + n2(p2 − ?̅?) (2)] ?̅?(1 − ?̅?)”
LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis (2016, methodology): “To date most of these types of analyses have been performed using genetic restricted maximum likelihood analysis (GREML) as implemented in software packages such as GCTA and LDAK (Yang et al, 2010; Yang et al, 2011; Lee et al, 2012; Speed et al. 2012).”
Estimating cross-population genetic correlations of causal effect sizes (2018, methodology): “We analyzed nine traits that were previously analyzed in Loh et al. (2015): allergic rhinitis, asthma, cardiovascular disease, type 2 diabetes (T2D), dyslipidemia, hypertension, macular degeneration, osteoarthritis, and osteoporosis.”
Detection and interpretation of shared genetic influences on 42 human traits (2016, positive): “This style of scan complements methods to quantify the “genetic correlation” between two traits 39;41;66;67 that are not generally concerned with identifying individual variants that influence both traits.”