Literature DB >> 21045869

Predicting genetic predisposition in humans: the promise of whole-genome markers.

Gustavo de los Campos1, Daniel Gianola, David B Allison.   

Abstract

Although genome-wide association studies have identified markers that are associated with various human traits and diseases, our ability to predict such phenotypes remains limited. A perhaps overlooked explanation lies in the limitations of the genetic models and statistical techniques commonly used in association studies. We propose that alternative approaches, which are largely borrowed from animal breeding, provide potential for advances. We review selected methods and discuss the challenges and opportunities ahead.

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Year:  2010        PMID: 21045869     DOI: 10.1038/nrg2898

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


  45 in total

1.  Best linear unbiased estimation and prediction under a selection model.

Authors:  C R Henderson
Journal:  Biometrics       Date:  1975-06       Impact factor: 2.571

Review 2.  Genomic medicine--a primer.

Authors:  Alan E Guttmacher; Francis S Collins
Journal:  N Engl J Med       Date:  2002-11-07       Impact factor: 91.245

Review 3.  Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations.

Authors:  Daniel J Schaid
Journal:  Hum Hered       Date:  2010-07-03       Impact factor: 0.444

4.  Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods.

Authors:  Gustavo De los Campos; Daniel Gianola; Guilherme J M Rosa; Kent A Weigel; José Crossa
Journal:  Genet Res (Camb)       Date:  2010-08       Impact factor: 1.588

5.  Predicting quantitative traits with regression models for dense molecular markers and pedigree.

Authors:  Gustavo de los Campos; Hugo Naya; Daniel Gianola; José Crossa; Andrés Legarra; Eduardo Manfredi; Kent Weigel; José Miguel Cotes
Journal:  Genetics       Date:  2009-03-16       Impact factor: 4.562

6.  Personal genomes: The case of the missing heritability.

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

7.  Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers.

Authors:  José Crossa; Gustavo de Los Campos; Paulino Pérez; Daniel Gianola; Juan Burgueño; José Luis Araus; Dan Makumbi; Ravi P Singh; Susanne Dreisigacker; Jianbing Yan; Vivi Arief; Marianne Banziger; Hans-Joachim Braun
Journal:  Genetics       Date:  2010-09-02       Impact factor: 4.562

8.  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

9.  A new estimate of family disease history providing improved prediction of disease risks.

Authors:  Rui Feng; Leslie A McClure; Hemant K Tiwari; George Howard
Journal:  Stat Med       Date:  2009-04-15       Impact factor: 2.373

10.  Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a Barley case study.

Authors:  Shengqiang Zhong; Jack C M Dekkers; Rohan L Fernando; Jean-Luc Jannink
Journal:  Genetics       Date:  2009-03-18       Impact factor: 4.562

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  142 in total

1.  GCTA: a tool for genome-wide complex trait analysis.

Authors:  Jian Yang; S Hong Lee; Michael E Goddard; Peter M Visscher
Journal:  Am J Hum Genet       Date:  2010-12-17       Impact factor: 11.025

2.  Why significant variables aren't automatically good predictors.

Authors:  Adeline Lo; Herman Chernoff; Tian Zheng; Shaw-Hwa Lo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-26       Impact factor: 11.205

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.  Complex Trait Prediction from Genome Data: Contrasting EBV in Livestock to PRS in Humans: Genomic Prediction.

Authors:  Naomi R Wray; Kathryn E Kemper; Benjamin J Hayes; Michael E Goddard; Peter M Visscher
Journal:  Genetics       Date:  2019-04       Impact factor: 4.562

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

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

7.  BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions.

Authors:  Meng Huang; Xiaolei Liu; Yao Zhou; Ryan M Summers; Zhiwu Zhang
Journal:  Gigascience       Date:  2019-02-01       Impact factor: 6.524

8.  Application of support vector regression to genome-assisted prediction of quantitative traits.

Authors:  Nanye Long; Daniel Gianola; Guilherme J M Rosa; Kent A Weigel
Journal:  Theor Appl Genet       Date:  2011-07-08       Impact factor: 5.699

9.  Explicit Modeling of Ancestry Improves Polygenic Risk Scores and BLUP Prediction.

Authors:  Chia-Yen Chen; Jiali Han; David J Hunter; Peter Kraft; Alkes L Price
Journal:  Genet Epidemiol       Date:  2015-05-21       Impact factor: 2.135

10.  Genetic Epidemiology of Complex Phenotypes.

Authors:  Darren D O'Rielly; Proton Rahman
Journal:  Methods Mol Biol       Date:  2021
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