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BACKGROUND The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships,(More)
The purpose of this study was to compare results obtained from various methodologies for genome-wide association studies, when applied to real data, in terms of number and commonality of regions identified and their genetic variance explained, computational speed, and possible pitfalls in interpretations of results. Methodologies include: two iteratively(More)
MOTIVATION Current methodology and software for quantitative trait loci (QTL) analyses do not use all available information and are inadequate to deal with the huge amount of QTL analyses to be needed in forecoming genetical genomics' studies. RESULTS We show that a mixed model statistical framework provides a very flexible tool for QTL modeling in a(More)
BACKGROUND Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. RESULTS Qxpak is a package for versatile statistical genomics, specifically designed for sophisticated(More)
  • Natalia S Forneris, Andres Legarra, Zulma G Vitezica, Shogo Tsuruta, Ignacio Aguilar, Ignacy Misztal +1 other
  • 2015
Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the(More)
Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and(More)
The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of(More)
Data included 393,097 calving ease, 129,520 gestation length, and 412,484 birth weight records on 412,484 Gelbvieh cattle. Additionally, pedigrees were available on 72,123 animals. Included in the models were effects of sex and age of dam, treated as fixed, as well as direct, maternal genetic and permanent environmental effects and effects of contemporary(More)
Many computations with SNP data including genomic evaluation, parameter estimation, and genome-wide association studies use an inverse of the genomic relationship matrix. The cost of a regular inversion is cubic and is prohibitively expensive for large matrices. Recent studies in cattle demonstrated that the inverse can be computed in almost linear time by(More)
The genomic relationship matrix (GRM) can be inverted by the algorithm for proven and young (APY) based on recursion on a random subset of animals. While a regular inverse has a cubic cost, the cost of the APY inverse can be close to linear. Theory for the APY assumes that the optimal size of the subset (maximizing accuracy of genomic predictions) is due to(More)