Literature DB >> 20877324

Reconciling the analysis of IBD and IBS in complex trait studies.

Joseph E Powell1, Peter M Visscher, Michael E Goddard.   

Abstract

Identity by descent (IBD) is a fundamental concept in genetics and refers to alleles that are descended from a common ancestor in a base population. Identity by state (IBS) simply refers to alleles that are the same, irrespective of whether they are inherited from a recent ancestor. In modern applications, IBD relationships are estimated from genetic markers in individuals without any known relationship. This can lead to erroneous inference because a consistent base population is not used. We argue that the purpose of most IBD calculations is to predict IBS at unobserved loci. Recognizing this aim leads to better methods to estimating IBD with benefits in mapping genes, estimating genetic variance and predicting inbreeding depression.

Entities:  

Mesh：

Year:  2010        PMID： 20877324     DOI： 10.1038/nrg2865

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  32 in total

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Authors:  K W Broman; J L Weber
Journal:  Am J Hum Genet       Date:  1999-12       Impact factor: 11.025

2.  Sequence-level population simulations over large genomic regions.

Authors:  Clive J Hoggart; Marc Chadeau-Hyam; Taane G Clark; Riccardo Lampariello; John C Whittaker; Maria De Iorio; David J Balding
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3.  Increased accuracy of artificial selection by using the realized relationship matrix.

Authors:  B J Hayes; P M Visscher; M E Goddard
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4.  Efficient methods to compute genomic predictions.

Authors:  P M VanRaden
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5.  Personal genomes: The case of the missing heritability.

Authors:  Brendan Maher
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

Review 6.  The genetics of inbreeding depression.

Authors:  Deborah Charlesworth; John H Willis
Journal:  Nat Rev Genet       Date:  2009-11       Impact factor: 53.242

7.  Common SNPs explain a large proportion of the heritability for human height.

Authors:  Jian Yang; Beben Benyamin; Brian P McEvoy; Scott Gordon; Anjali K Henders; Dale R Nyholt; Pamela A Madden; Andrew C Heath; Nicholas G Martin; Grant W Montgomery; Michael E Goddard; Peter M Visscher
Journal:  Nat Genet       Date:  2010-06-20       Impact factor: 38.330

8.  Detection of sharing by descent, long-range phasing and haplotype imputation.

Authors:  Augustine Kong; Gisli Masson; Michael L Frigge; Arnaldur Gylfason; Pasha Zusmanovich; Gudmar Thorleifsson; Pall I Olason; Andres Ingason; Stacy Steinberg; Thorunn Rafnar; Patrick Sulem; Magali Mouy; Frosti Jonsson; Unnur Thorsteinsdottir; Daniel F Gudbjartsson; Hreinn Stefansson; Kari Stefansson
Journal:  Nat Genet       Date:  2008-09       Impact factor: 38.330

9.  Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches.

Authors:  A D Carothers; I Rudan; I Kolcic; O Polasek; C Hayward; A F Wright; H Campbell; P Teague; N D Hastie; J L Weber
Journal:  Ann Hum Genet       Date:  2006-09       Impact factor: 1.670

10.  Population structure and eigenanalysis.

Authors:  Nick Patterson; Alkes L Price; David Reich
Journal:  PLoS Genet       Date:  2006-12       Impact factor: 5.917
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  149 in total

1.  Inbreeding causes early death in a passerine bird.

Authors:  N L Hemmings; J Slate; T R Birkhead
Journal:  Nat Commun       Date:  2012-05-29       Impact factor: 14.919

2.  Integrating Nonadditive Genomic Relationship Matrices into the Study of Genetic Architecture of Complex Traits.

Authors:  Alireza Nazarian; Salvador A Gezan
Journal:  J Hered       Date:  2015-12-27       Impact factor: 2.645

3.  An Equation to Predict the Accuracy of Genomic Values by Combining Data from Multiple Traits, Populations, or Environments.

Authors:  Yvonne C J Wientjes; Piter Bijma; Roel F Veerkamp; Mario P L Calus
Journal:  Genetics       Date:  2015-12-04       Impact factor: 4.562

Review 4.  Mapping QTL for agronomic traits in breeding populations.

Authors:  Tobias Würschum
Journal:  Theor Appl Genet       Date:  2012-05-22       Impact factor: 5.699

5.  Back to basics for Bayesian model building in genomic selection.

Authors:  Hanni P Kärkkäinen; Mikko J Sillanpää
Journal:  Genetics       Date:  2012-05-02       Impact factor: 4.562

Review 6.  Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction.

Authors:  William G Hill
Journal:  Genetics       Date:  2014-01       Impact factor: 4.562

Review 7.  Identity by descent: variation in meiosis, across genomes, and in populations.

Authors:  Elizabeth A Thompson
Journal:  Genetics       Date:  2013-06       Impact factor: 4.562

8.  Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium.

Authors:  Pascal Schopp; Dominik Müller; Frank Technow; Albrecht E Melchinger
Journal:  Genetics       Date:  2016-11-09       Impact factor: 4.562

9.  Estimating missing heritability for disease from genome-wide association studies.

Authors:  Sang Hong Lee; Naomi R Wray; Michael E Goddard; Peter M Visscher
Journal:  Am J Hum Genet       Date:  2011-03-03       Impact factor: 11.025

10.  A general definition of the heritable variation that determines the potential of a population to respond to selection.

Authors:  Piter Bijma
Journal:  Genetics       Date:  2011-09-16       Impact factor: 4.562
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