Linkage Disequilibrium and Its Expectation in Human Populations

Sved, J. A.

doi:10.1375/twin.12.1.35

Cited by 11 publications

(12 citation statements)

References 54 publications

(61 reference statements)

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“…First, some causal variants might have different effects across ethnicities (e.g., because of differences in environmental or genetic backgrounds), and some might be population specific if they arose or were lost after the European-African divergence thought to have occurred 50-100K years ago. [28][29][30] Our finding that high-MAF SNPs show greater SNP correlations than low-MAF SNPs lends some support to the hypothesis that lower-MAF schizophrenia causal variants are increasingly population specific and/or are differentially tagged by SNPs across ethnicities. Second, lower SNP correlations should occur to the degree that LD between causal variants and the SNPs that predict them differs across ethnicity.…”

Section: Discussionmentioning

confidence: 53%

Additive Genetic Variation in Schizophrenia Risk Is Shared by Populations of African and European Descent

Candia

Lee

Yang

et al. 2013

The American Journal of Human Genetics

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To investigate the extent to which the proportion of schizophrenia's additive genetic variation tagged by SNPs is shared by populations of European and African descent, we analyzed the largest combined African descent (AD [n = 2,142]) and European descent (ED [n = 4,990]) schizophrenia case-control genome-wide association study (GWAS) data set available, the Molecular Genetics of Schizophrenia (MGS) data set. We show how a method that uses genomic similarities at measured SNPs to estimate the additive genetic correlation (SNP correlation [SNP-rg]) between traits can be extended to estimate SNP-rg for the same trait between ethnicities. We estimated SNP-rg for schizophrenia between the MGS ED and MGS AD samples to be 0.66 (SE = 0.23), which is significantly different from 0 (p(SNP-rg = 0) = 0.0003), but not 1 (p(SNP-rg = 1) = 0.26). We re-estimated SNP-rg between an independent ED data set (n = 6,665) and the MGS AD sample to be 0.61 (SE = 0.21, p(SNP-rg = 0) = 0.0003, p(SNP-rg = 1) = 0.16). These results suggest that many schizophrenia risk alleles are shared across ethnic groups and predate African-European divergence.

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Section: Discussionmentioning

confidence: 53%

Additive Genetic Variation in Schizophrenia Risk Is Shared by Populations of African and European Descent

Candia

Lee

Yang

et al. 2013

The American Journal of Human Genetics

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“…Besides D, several measures of LD (for example, D', l, d, r 2 , c 2 r 2 , among others) have been suggested (Lewontin, 1964;Bengtsson and Thomson, 1981;Hill and Weir, 1994;Terwilliger, 1995;Zhao et al, 2005;Gianola et al, 2013). The merits, comparison, and methodologies of these metrics with the utilization of biallelic or multi-allelic loci have been extensively described in the literature (e.g., Jorde, 2000;Pritchard and Przeworski, 2001;Mueller, 2004;Sved, 2009). Choosing the appropriate LD measure depends on the objective of the study, and one may perform better than another in particular situations.…”

Section: A Historical Glancementioning

confidence: 99%

On the Extent of Linkage Disequilibrium in the Genome of Farm Animals

Qanbari

2020

Front. Genet.

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Given the importance of linkage disequilibrium (LD) in gene mapping and evolutionary inferences, I characterize in this review the pattern of LD and discuss the influence of human intervention during domestication, breed establishment, and subsequent genetic improvement on shaping the genome of livestock species. To this end, I summarize data on the profile of LD based on array genotypes vs. sequencing data in cattle and chicken, two major livestock species, and compare to the human case. This comparison provides insights into the real dimension of the pairwise allelic correlation and haplo-block structuring. The dependency of LD on allelic frequency is pictured and a recently introduced metric for moderating it is outlined. In the context of the contact farm animals had with human, the impact of genetic forces including admixture, mutation, recombination rate, selection, and effective population size on LD is discussed. The review further highlights the interplay of LD with runs of homozygosity and concludes with the operational implications of the widely used association and selection mapping studies in relation to LD.

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“…In this case, the fraction of gene variance explained by the SNP is r 2 (although the LD and the gene variance remains unknown until the causative gene itself is identified). The expectation of r 2 can be expressed as E r 2 = 1 (1 + 4N e c), with N e being the effective population size, and c denotes the recombination rate between the two loci (Sved, 2009;Tenesa et al, 2007). From this expression, it becomes obvious that the expected LD decays fast with increasing distances between loci, especially if the effective population size is large.…”

Section: Introductionmentioning

confidence: 99%

Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs

Schmid

Bennewitz

2017

Arch. Anim. Breed.

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Abstract. Quantitative or complex traits are controlled by many genes and environmental factors. Most traits in livestock breeding are quantitative traits. Mapping genes and causative mutations generating the genetic variance of these traits is still a very active area of research in livestock genetics. Since genome-wide and dense SNP panels are available for most livestock species, genome-wide association studies (GWASs) have become the method of choice in mapping experiments. Different statistical models are used for GWASs. We will review the frequently used single-marker models and additionally describe Bayesian multi-marker models. The importance of nonadditive genetic and genotype-by-environment effects along with GWAS methods to detect them will be briefly discussed. Different mapping populations are used and will also be reviewed. Whenever possible, our own real-data examples are included to illustrate the reviewed methods and designs. Future research directions including post-GWAS strategies are outlined.

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Linkage Disequilibrium and Its Expectation in Human Populations

Cited by 11 publications

References 54 publications

Additive Genetic Variation in Schizophrenia Risk Is Shared by Populations of African and European Descent

Additive Genetic Variation in Schizophrenia Risk Is Shared by Populations of African and European Descent

On the Extent of Linkage Disequilibrium in the Genome of Farm Animals

Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs

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