scholarly journals Relationship between LD Score and Haseman-Elston Regression

2015 ◽  
Author(s):  
Brendan Bulik-Sullivan
Keyword(s):  
Variance Component ◽  
State Of The Art ◽  
Case Control ◽  
Genotype Data ◽  
Summary Statistics ◽  
Mathematical Relationship ◽  
Individual Genotype ◽  
Variance Component Models ◽  
Component Models ◽  
Summary Data

Estimating SNP-heritability from summary statistics using LD Score regression provides a convenient alternative to standard variance component models, because LD Score regression is computationally very fast and does not require individual genotype data. However, the mathematical relationship between variance component methods and LD Score regression is not clear; in particular, it is not known in general how much of an increase in standard error one incurs by working with summary data instead of individual genotypes. In this paper, I show that in samples of unrelated individuals, LD Score regression with constrained intercept is essentially the same as Haseman-Elston (HE) regression, which is currently the state-of-the-art method for estimating SNP-heritability from ascertained case/control samples. Similar results hold for SNP-genetic correlation.

The Analytic Identification of Variance Component Models Common to Behavior Genetics

2021 ◽  
Author(s):  
Michael D. Hunter ◽  
S. Mason Garrison ◽  
S. Alexandra Burt ◽  
Joseph L. Rodgers
Keyword(s):  
Variance Component ◽  
Behavior Genetics ◽  
Variance Component Models ◽  
Component Models

Bayesian Methods for Variance Component Models

1996 ◽  
Vol 91 (434) ◽  
pp. 743-752 ◽  
Author(s):  
Li Sun ◽  
John S. J. Hsu ◽  
Irwin Guttman ◽  
Tom Leonard
Keyword(s):  
Bayesian Methods ◽  
Variance Component ◽  
Variance Component Models ◽  
Component Models

scholarly journals How to deal with genotype uncertainty in variance component quantitative trait loci analyses

2011 ◽  
Vol 93 (5) ◽  
pp. 333-342 ◽  
Author(s):  
XIA SHEN ◽  
LARS RÖNNEGÅRD ◽  
ÖRJAN CARLBORG
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Variance Component ◽  
Large Animal ◽  
Trait Loci ◽  
Sib Families ◽  
Variance Component Estimates ◽  
Variance Component Models ◽  
Component Models

SummaryDealing with genotype uncertainty is an ongoing issue in genetic analyses of complex traits. Here we consider genotype uncertainty in quantitative trait loci (QTL) analyses for large crosses in variance component models, where the genetic information is included in identity-by-descent (IBD) matrices. An IBD matrix is one realization from a distribution of potential IBD matrices given available marker information. In QTL analyses, its expectation is normally used resulting in potentially reduced accuracy and loss of power. Previously, IBD distributions have been included in models for small human full-sib families. We develop an Expectation–Maximization (EM) algorithm for estimating a full model based on Monte Carlo imputation for applications in large animal pedigrees. Our simulations show that the bias of variance component estimates using traditional expected IBD matrix can be adjusted by accounting for the distribution and that the calculations are computationally feasible for large pedigrees.

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