Pitfalls of predicting complex traits from SNPs

被引：511

作者：

Wray, Naomi R. ^{[1
]}

Yang, Jian ^{[1
,2
]}

Hayes, Ben J. ^{[3
,4
,5
]}

Price, Alkes L. ^{[6
,7
,8
,9
]}

Goddard, Michael E. ^{[3
]}

Visscher, Peter M. ^{[1
,2
]}

机构：

[1] Univ Queensland, Queensland Brain Inst, St Lucia, Qld 4071, Australia

[2] Univ Queensland, Diamantina Inst, Translat Res Inst, Woolloongabba, Qld 4102, Australia

[3] Dept Primary Ind, Biosci Res Div, Melbourne, Vic 3001, Australia

[4] La Trobe Univ, Dairy Futures Cooperat Res Ctr, AgriBio, Ctr AgriBiosci, Bundoora, Vic 3083, Australia

[5] La Trobe Univ, Bundoora, Vic 3086, Australia

[6] Harvard Univ, Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA

[7] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[8] Broad MIT Inst & Harvard, Cambridge, MA 02142 USA

[9] Harvard Univ, Sch Publ Hlth, Program Mol & Genet Epidemiol, Boston, MA 02115 USA

来源：

NATURE REVIEWS GENETICS | 2013年 / 14卷 / 07期

关键词：

GENOME-WIDE ASSOCIATION; RISK PREDICTION; GENETIC RISK; QUANTITATIVE TRAITS; SUSCEPTIBILITY LOCI; SENSATION SEEKING; NATURAL-SELECTION; LARGE PROPORTION; DOPAMINE GENES; VARIANTS;

D O I：

10.1038/nrg3457

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The success of genome-wide association studies (GWASs) has led to increasing interest in making predictions of complex trait phenotypes, including disease, from genotype data. Rigorous assessment of the value of predictors is crucial before implementation. Here we discuss some of the limitations and pitfalls of prediction analysis and show how naive implementations can lead to severe bias and misinterpretation of results.

引用

页码：507 / 515

页数：9

共 81 条

[1] SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction [J].

Abraham, Gad ;

Kowalczyk, Adam ;

Zobel, Justin ;

Inouye, Michael .

BMC BIOINFORMATICS, 2012, 13

[2] Hundreds of variants clustered in genomic loci and biological pathways affect human height [J].

Allen, Hana Lango ;

Estrada, Karol ;

Lettre, Guillaume ;

Berndt, Sonja I. ;

Weedon, Michael N. ;

Rivadeneira, Fernando ;

Willer, Cristen J. ;

Jackson, Anne U. ;

Vedantam, Sailaja ;

Raychaudhuri, Soumya ;

Ferreira, Teresa ;

Wood, Andrew R. ;

Weyant, Robert J. ;

Segre, Ayellet V. ;

Speliotes, Elizabeth K. ;

Wheeler, Eleanor ;

Soranzo, Nicole ;

Park, Ju-Hyun ;

Yang, Jian ;

Gudbjartsson, Daniel ;

Heard-Costa, Nancy L. ;

Randall, Joshua C. ;

Qi, Lu ;

Smith, Albert Vernon ;

Maegi, Reedik ;

Pastinen, Tomi ;

Liang, Liming ;

Heid, Iris M. ;

Luan, Jian'an ;

Thorleifsson, Gudmar ;

Winkler, Thomas W. ;

Goddard, Michael E. ;

Lo, Ken Sin ;

Palmer, Cameron ;

Workalemahu, Tsegaselassie ;

Aulchenko, Yurii S. ;

Johansson, Asa ;

Zillikens, M. Carola ;

Feitosa, Mary F. ;

Esko, Tonu ;

Johnson, Toby ;

Ketkar, Shamika ;

Kraft, Peter ;

Mangino, Massimo ;

Prokopenko, Inga ;

Absher, Devin ;

Albrecht, Eva ;

Ernst, Florian ;

Glazer, Nicole L. ;

Hayward, Caroline .

NATURE, 2010, 467 (7317) :832-838

[3] Selection bias in gene extraction on the basis of microarray gene-expression data [J].

Ambroise, C ;

McLachlan, GJ .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (10) :6562-6566

[4] Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants [J].

Ayodo, George ;

Price, Alkes L. ;

Keinan, Alon ;

Ajwang, Arthur ;

Otieno, Michael F. ;

Orago, Alloys S. S. ;

Patterson, Nick ;

Reich, David .

AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (02) :234-242

[5] Comparison of Statistical Tests for Association between Rare Variants and Binary Traits [J].

Bacanu, Silviu-Alin ;

Nelson, Matthew R. ;

Whittaker, John C. .

PLOS ONE, 2012, 7 (08)

[6] Natural selection has driven population differentiation in modern humans [J].

Barreiro, Luis B. ;

Laval, Guillaume ;

Quach, Helene ;

Patin, Etienne ;

Quintana-Murci, Lluis .

NATURE GENETICS, 2008, 40 (03) :340-345

[7] Genetic testing and common disorders in a public health framework: how to assess relevance and possibilities Background Document to the ESHG recommendations on genetic testing and common disorders [J].

Becker, Frauke ;

van El, Carla G. ;

Ibarreta, Dolores ;

Zika, Eleni ;

Hogarth, Stuart ;

Borry, Pascal ;

Cambon-Thomsen, Anne ;

Cassiman, Jean Jacques ;

Evers-Kiebooms, Gerry ;

Hodgson, Shirley ;

Janssens, A. Cecile J. W. ;

Kaariainen, Helena ;

Krawczak, Michael ;

Kristoffersson, Ulf ;

Lubinski, Jan ;

Patch, Christine ;

Penchaszadeh, Victor B. ;

Read, Andrew ;

Rogowski, Wolf ;

Sequeiros, Jorge ;

Tranebjaerg, Lisbeth ;

van Langen, Irene M. ;

Wallace, Helen ;

Zimmern, Ron ;

Schmidtke, Joerg ;

Cornel, Martina C. .

EUROPEAN JOURNAL OF HUMAN GENETICS, 2011, 19 :S6-S44

[8] Population structure confounds autism genetic classifier [J].

Belgard, T. G. ;

Jankovic, I. ;

Lowe, J. K. ;

Geschwind, D. H. .

MOLECULAR PSYCHIATRY, 2014, 19 (04) :405-407

[9] Predicting mutation outcome from early stochastic variation in genetic interaction partners [J].

Burga, Alejandro ;

Olivia Casanueva, M. ;

Lehner, Ben .

NATURE, 2011, 480 (7376) :250-U133

[10] Demonstrating stratification in a European American population [J].

Campbell, CD ;

Ogburn, EL ;

Lunetta, KL ;

Lyon, HN ;

Freedman, ML ;

Groop, LC ;

Altshuler, D ;

Ardlie, KG ;

Hirschhorn, JN .

NATURE GENETICS, 2005, 37 (08) :868-872

← 1 2 3 4 5 6 7 8 9 →