Regularized Machine Learning in the Genetic Prediction of Complex Traits
[...]we discuss some key future advances, open questions and challenges in this developing field, when moving toward low-frequency variants and cross-phenotype interactions. Multivariate modeling approaches have already been shown to provide improved insights into genetic mechanisms and the intera...
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| Veröffentlicht in: | PLoS genetics Jg. 10; H. 11; S. e1004754 |
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| Hauptverfasser: | , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
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United States
Public Library of Science
01.11.2014
Public Library of Science (PLoS) |
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| ISSN: | 1553-7404, 1553-7390, 1553-7404 |
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| Abstract |
[...]we discuss some key future advances, open questions and challenges in this developing field, when moving toward low-frequency variants and cross-phenotype interactions. Multivariate modeling approaches have already been shown to provide improved insights into genetic mechanisms and the interaction networks behind many complex traits, including atherosclerosis, coronary heart disease, and lipid levels, which would have gone undetected using the standard univariate modeling [2], [19]-[22]. |
|---|---|
| AbstractList |
[...]we discuss some key future advances, open questions and challenges in this developing field, when moving toward low-frequency variants and cross-phenotype interactions. Multivariate modeling approaches have already been shown to provide improved insights into genetic mechanisms and the interaction networks behind many complex traits, including atherosclerosis, coronary heart disease, and lipid levels, which would have gone undetected using the standard univariate modeling [2], [19]-[22]. |
| Audience | Academic |
| Author | Airola, Antti Okser, Sebastian Ripatti, Samuli Pahikkala, Tapio Salakoski, Tapio Aittokallio, Tero |
| AuthorAffiliation | 2 Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland 4 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland 5 Wellcome Trust Sanger Institute, Hinxton, United Kingdom 3 Hjelt Institute, University of Helsinki, Helsinki, Finland 1 Department of Information Technology, University of Turku, Turku, Finland University of California San Diego and The Scripps Research Institute, United States of America |
| AuthorAffiliation_xml | – name: 1 Department of Information Technology, University of Turku, Turku, Finland – name: 4 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland – name: 3 Hjelt Institute, University of Helsinki, Helsinki, Finland – name: University of California San Diego and The Scripps Research Institute, United States of America – name: 2 Turku Centre for Computer Science (TUCS), University of Turku and Åbo Akademi University, Turku, Finland – name: 5 Wellcome Trust Sanger Institute, Hinxton, United Kingdom |
| Author_xml | – sequence: 1 givenname: Sebastian surname: Okser fullname: Okser, Sebastian – sequence: 2 givenname: Tapio surname: Pahikkala fullname: Pahikkala, Tapio – sequence: 3 givenname: Antti surname: Airola fullname: Airola, Antti – sequence: 4 givenname: Tapio surname: Salakoski fullname: Salakoski, Tapio – sequence: 5 givenname: Samuli surname: Ripatti fullname: Ripatti, Samuli – sequence: 6 givenname: Tero surname: Aittokallio fullname: Aittokallio, Tero |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25393026$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1002/gepi.20509 10.1038/ng0710-558 10.1093/bioinformatics/bts669 10.3389/fgene.2012.00026 10.1371/journal.pgen.1000432 10.1534/genetics.113.153221 10.1186/1471-2105-12-S1-S10 10.1371/journal.pgen.1002973 10.1093/hmg/ddr378 10.1038/ng.2644 10.1093/bioinformatics/btp041 10.1093/bioinformatics/bts015 10.1093/bioinformatics/btq688 10.1093/bioinformatics/btt139 10.1371/journal.pgen.1002685 10.1023/A:1010933404324 10.1038/nrg3404 10.1371/journal.pgen.1003396 10.1038/nrg3523 10.1038/nrg2809 10.1016/S0140-6736(10)60452-7 10.1371/journal.pgen.1002907 10.1038/nrg2516 10.1186/1471-2156-11-49 10.1111/j.2517-6161.1996.tb02080.x 10.1242/jeb.002311 10.1080/01621459.1988.10478694 10.1371/journal.pgen.1000678 10.1371/journal.pgen.1003010 10.1371/journal.pone.0093379 10.1371/journal.pone.0029115 10.1371/journal.pcbi.1003101 10.1371/journal.pgen.1003959 10.1371/journal.pgen.1003264 10.1371/journal.pcbi.1003200 10.1371/journal.pgen.1003608 10.3389/fgene.2013.00270 10.1109/TCBB.2012.80 10.1002/gepi.20473 10.1093/bioinformatics/btq600 10.1016/j.cell.2011.03.020 10.1186/gm480 10.1038/nrg2579 10.1161/CIRCGENETICS.113.000387 10.1093/bioinformatics/btp713 10.1371/journal.pgen.1000130 10.1038/msb.2013.2 10.1038/456018a 10.1016/j.ajhg.2013.05.002 10.3389/fgene.2012.00097 10.1093/bib/bbr053 10.1038/ng.2579 10.1038/ng.608 10.1186/1756-0381-6-6 10.1002/gepi.20556 10.1534/genetics.111.128694 10.1016/j.ajhg.2009.08.006 10.1038/nature12170 10.1016/j.jmb.2013.07.038 10.1186/1748-7188-7-11 10.3389/fgene.2012.00176 10.1016/S0140-6736(10)61267-6 10.1093/bioinformatics/btu140 10.1002/gepi.21698 10.1016/j.ajhg.2013.04.004 10.1016/j.tig.2009.12.008 10.1093/ije/dys183 10.3389/fgene.2013.00051 10.1038/nrg3461 10.1186/1756-0381-6-5 10.1016/j.tig.2012.07.001 10.1093/bib/bbs024 10.1038/nrg3118 10.1371/journal.pcbi.1002822 10.1038/nrg3552 10.1016/j.neuroimage.2012.08.002 10.1038/nature05911 10.1038/nrg3457 10.1515/sagmb-2012-0032 10.1016/j.tig.2011.05.007 10.1101/gr.169375.113 10.1186/1471-2105-14-61 10.1371/journal.pgen.1002051 10.1016/j.ajhg.2007.10.012 10.1371/journal.pgen.1003041 10.1093/bioinformatics/btt081 10.1093/bib/bbr075 10.1371/journal.pone.0093017 10.1111/j.1742-4658.2012.08810.x 10.1371/journal.pgen.1003939 10.1038/nature11867 10.1023/A:1025667309714 10.1007/s00439-012-1194-y 10.1016/j.copbio.2013.03.004 10.1186/gm464 10.1111/j.1467-9868.2005.00503.x 10.1002/gepi.21762 10.1093/bioinformatics/bts335 10.1093/bioinformatics/btq448 10.1016/j.gde.2010.10.009 10.1371/journal.pgen.1000337 10.1093/hmg/ddp295 10.1038/ng.2876 10.1002/gepi.21777 10.1371/journal.pgen.1003657 10.1162/neco.2008.05-07-517 10.1186/1471-2105-13-88 10.1186/1471-2105-10-78 10.1534/genetics.113.150078 10.1371/journal.pgen.1001146 10.1371/journal.pgen.1003348 |
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| Copyright | COPYRIGHT 2014 Public Library of Science 2014 Okser et al 2014 Okser et al 2014 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Okser S, Pahikkala T, Airola A, Salakoski T, Ripatti S, Aittokallio T (2014) Regularized Machine Learning in the Genetic Prediction of Complex Traits. PLoS Genet 10(11): e1004754. doi:10.1371/journal.pgen.1004754 |
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| References | G Bebek (ref74) 2012; 13 V Wimmer (ref115) 2013; 195 M Inouye (ref19) 2012; 8 BA McKinney (ref103) 2009; 5 U Ober (ref114) 2012; 8 C Lu (ref77) 2013; 29 TJ Mitchell (ref100) 1998; 83 (ref45) 2013; 45 JS1 Bloom (ref44) 2013; 494 G Gibson (ref57) 2013; 5 G de Los Campos (ref61) 2013; 9 (ref118) 2007; 447 MJ Machiela (ref55) 2011; 35 X Sun (ref80) 2014; 5 YA Meng (ref108) 2009; 10 F Pedregosa (ref119) 2011; 12 GW Carter (ref72) 2012; 8 Z Wei (ref1) 2009; 5 HJ Cordell (ref17) 2009; 10 M Silver (ref22) 2013; 9 Q He (ref111) 2011; 27 R Brough (ref16) 2011; 21 D Urbach (ref56) 2012; 28 G Shi (ref26) 2011; 35 H Zou (ref83) 2003; 67 Y Zhao (ref104) 2012; 41 L Breiman (ref90) 2001; 45 R Che (ref23) 2013; 4 CB Moore (ref42) 2013; 9 G Abraham (ref24) 2013; 37 F Dudbridge (ref32) 2013; 9 TA Manolio (ref11) 2013; 14 S Ripatti (ref20) 2012; 376 R Upstill-Goddard (ref76) 2013; 14 Y Huang (ref51) 2013; 4 T Peltola (ref94) 2012; 7 G Abraham (ref87) 2012; 13 AL Boulesteix (ref92) 2012; 13 P Kraft (ref9) 2009; 10 KA Hunt (ref40) 2013; 498 Z1 Wei (ref4) 2013; 92 J Yang (ref106) 2014; 46 NR Wray (ref28) 2013; 14 S Okser (ref2) 2009; 6 O Manor (ref52) 2013; 9 JH Moore (ref14) 2009; 85 CM Mutshinda (ref67) 2012; 3 M Hajiloo (ref107) 2013; 14 J Kruppa (ref3) 2012; 131 T Pahikkala (ref30) 2012; 7 B Lehner (ref13) 2007; 210 NE Wineinger (ref21) 2013; 4 P Marttinen (ref66) 2013; 12 C Su (ref78) 2013; 6 J Li (ref93) 2011; 27 L Bottolo (ref70) 2013; 9 M Silver (ref64) 2012; 63 SW Hartley (ref68) 2012; 3 WS Bush (ref79) 2012; 8 V Botta (ref109) 2014; 9 M Robnik-Sikonja (ref101) 2003; 53 EE Eichler (ref37) 2010; 11 CJ Hoggart (ref86) 2008; 4 A Galvan (ref54) 2010; 26 B Lehner (ref12) 2011; 27 K Mitra (ref75) 2013; 14 N Solovieff (ref63) 2013; 14 O Manor (ref41) 2013; 9 L Jostins (ref29) 2011; 20 SW Hartley (ref69) 2013; 29 V Wimmer (ref113) 2012; 28 R Tibshirani (ref82) 1994; 58 J Jakobsdottir (ref27) 2009; 5 DM Evans (ref25) 2009; 18 G Gibson (ref38) 2012; 13 X Zhou (ref95) 2013; 9 B Rakitsch (ref105) 2013; 29 G Gibson (ref18) 2010; 42 LL Gerfo (ref99) 2008; 20 R Makowsky (ref35) 2011; 7 GE Hoffman (ref89) 2013; 9 Z Zhang (ref116) 2014; 9 JH Moore (ref7) 2010; 26 ED Schifano (ref65) 2013; 92 A Burga (ref46) 2012; 279 J Yang (ref34) 2010; 42 A Burga (ref49) 2013; 24 P Sebastiani (ref81) 2012; 3 CB Do (ref33) 2012; 8 TT Wu (ref85) 2009; 25 P Marttinen (ref71) 2014; 30 D Speed (ref117) 2014; 24 P Yang (ref102) 2011; 12 GK Chen (ref88) 2012; 28 N Chatterjee (ref31) 2013; 45 Y Bromberg (ref58) 2013; 425 YA Kim (ref73) 2012; 3 B Maher (ref36) 2008; 456 R Mihaescu (ref39) 2013; 20 S Szymczak (ref6) 2009; 33 A Goldinger (ref53) 2013; 195 T Poggio (ref98) 2002 P Waldmann (ref84) 2013; 4 J Wu (ref59) 2013; 37 H Zhou (ref43) 2010; 26 C Queitsch (ref48) 2012; 8 H Warren (ref60) 2014; 38 C Kooperberg (ref8) 2010; 34 B Lehner (ref47) 2013; 14 BA Goldstein (ref91) 2010; 11 EA Ashley (ref10) 2010; 375 PH Hennings-Yeomans (ref62) 2012; 9 JN Milton (ref96) 2014; 7 U Ober (ref112) 2011; 188 A Ashworth (ref15) 2011; 145 S Park (ref50) 2013; 9 S Okser (ref5) 2013; 6 N Malo (ref110) 2008; 82 G Brown (ref97) 2005; 6 |
| References_xml | – volume: 34 start-page: 643 year: 2010 ident: ref8 article-title: Risk prediction using genome-wide association studies publication-title: Genet Epidemiol doi: 10.1002/gepi.20509 – volume: 42 start-page: 558 year: 2010 ident: ref18 article-title: Hints of hidden heritability in GWAS publication-title: Nat Genet doi: 10.1038/ng0710-558 – volume: 29 start-page: 206 year: 2013 ident: ref105 article-title: A Lasso multi-marker mixed model for association mapping with population structure correction publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts669 – volume: 3 start-page: 26 year: 2012 ident: ref81 article-title: Naive Bayesian classifier and genetic risk score for genetic risk prediction of a categorical trait: not so different after all! publication-title: Front Genet doi: 10.3389/fgene.2012.00026 – volume: 5 start-page: e1000432 year: 2009 ident: ref103 article-title: Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis publication-title: PLoS Genet doi: 10.1371/journal.pgen.1000432 – volume: 195 start-page: 1117 year: 2013 ident: ref53 article-title: Genetic and Non-Genetic Variation Revealed for the Principal Components of Human Gene Expression publication-title: Genetics doi: 10.1534/genetics.113.153221 – volume: 12 start-page: S10 year: 2011 ident: ref102 article-title: Gene-gene interaction filtering with ensemble of filters publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-S1-S10 – volume: 3 start-page: 227 year: 2012 ident: ref73 article-title: Bridging the gap between genotype and phenotype via network approaches publication-title: Front Genet – volume: 8 start-page: e1002973 year: 2012 ident: ref33 article-title: Comparison of family history and SNPs for predicting risk of complex disease publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002973 – volume: 20 start-page: R182 year: 2011 ident: ref29 article-title: Genetic risk prediction in complex disease publication-title: Hum Mol Genet doi: 10.1093/hmg/ddr378 – volume: 45 start-page: 767 year: 2013 ident: ref45 article-title: Combined sequence-based and genetic mapping analysis of complex traits in outbred rats publication-title: Nat Genet doi: 10.1038/ng.2644 – volume: 25 start-page: 714 year: 2009 ident: ref85 article-title: Genome-wide association analysis by lasso penalized logistic regression publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp041 – volume: 28 start-page: 719 year: 2012 ident: ref88 article-title: A scalable and portable framework for massively parallel variable selection in genetic association studies publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts015 – volume: 27 start-page: 516 year: 2011 ident: ref93 article-title: The Bayesian lasso for genome-wide association studies publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq688 – volume: 29 start-page: 1241 year: 2013 ident: ref77 article-title: Network-guided sparse regression modeling for detection of gene-by-gene interactions publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt139 – volume: 8 start-page: e1002685 year: 2012 ident: ref114 article-title: Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002685 – volume: 45 start-page: 5 year: 2001 ident: ref90 article-title: Random Forests publication-title: Machine Learning doi: 10.1023/A:1010933404324 – volume: 14 start-page: 168 year: 2013 ident: ref47 article-title: Genotype to phenotype: lessons from model organisms for human genetics publication-title: Nat Rev Genet doi: 10.1038/nrg3404 – volume: 9 start-page: e1003396 year: 2013 ident: ref52 article-title: Robust prediction of expression differences among human individuals using only genotype information publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003396 – volume: 14 start-page: 549 year: 2013 ident: ref11 article-title: Bringing genome-wide association findings into clinical use publication-title: Nat Rev Genet doi: 10.1038/nrg3523 – volume: 11 start-page: 446 year: 2010 ident: ref37 article-title: Missing heritability and strategies for finding the underlying causes of complex disease publication-title: Nat Rev Genet doi: 10.1038/nrg2809 – volume: 375 start-page: 1525 year: 2010 ident: ref10 article-title: Clinical assessment incorporating a personal genome publication-title: Lancet doi: 10.1016/S0140-6736(10)60452-7 – volume: 8 start-page: e1002907 year: 2012 ident: ref19 article-title: Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002907 – volume: 5 start-page: 106 year: 2014 ident: ref80 article-title: Analysis pipeline for the epistasis search - statistical versus biological filtering publication-title: Front Genet – volume: 10 start-page: 264 year: 2009 ident: ref9 article-title: Beyond odds ratios: communicating disease risk based on genetic profiles publication-title: Nat Rev Genet doi: 10.1038/nrg2516 – volume: 11 start-page: 49 year: 2010 ident: ref91 article-title: An application of Random Forests to a genome-wide association dataset: methodological considerations and new findings publication-title: BMC Genet doi: 10.1186/1471-2156-11-49 – volume: 58 start-page: 267 year: 1994 ident: ref82 article-title: Regression shrinkage and selection via the Lasso publication-title: J Royal Stat Soc B doi: 10.1111/j.2517-6161.1996.tb02080.x – volume: 210 start-page: 1559 year: 2007 ident: ref13 article-title: Modelling genotype-phenotype relationships and human disease with genetic interaction networks publication-title: J Exp Biol doi: 10.1242/jeb.002311 – volume: 83 start-page: 1023 year: 1998 ident: ref100 article-title: Bayesian variable selection in linear regression publication-title: J Am Stat Assoc doi: 10.1080/01621459.1988.10478694 – volume: 5 start-page: e1000678 year: 2009 ident: ref1 article-title: From disease association to risk assessment: an optimistic view from genome-wide association studies on type 1 diabetes publication-title: PLoS Genet doi: 10.1371/journal.pgen.1000678 – volume: 8 start-page: e1003010 year: 2012 ident: ref72 article-title: Use of pleiotropy to model genetic interactions in a population publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003010 – volume: 9 start-page: e93379 year: 2014 ident: ref109 article-title: Exploiting SNP correlations within random forest for genome-wide association studies publication-title: PloS ONE doi: 10.1371/journal.pone.0093379 – volume: 7 start-page: e29115 year: 2012 ident: ref94 article-title: Bayesian variable selection in searching for additive and dominant effects in genome-wide data publication-title: PLoS ONE doi: 10.1371/journal.pone.0029115 – volume: 9 start-page: e1003101 year: 2013 ident: ref89 article-title: PUMA: a unified framework for penalized multiple regression analysis of GWAS data publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1003101 – volume: 9 start-page: e1003959 year: 2013 ident: ref42 article-title: Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003959 – volume: 9 start-page: e1003264 year: 2013 ident: ref95 article-title: Polygenic modeling with Bayesian sparse linear mixed models publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003264 – volume: 9 start-page: e1003200 year: 2013 ident: ref41 article-title: Predicting disease risk using bootstrap ranking and classification algorithms publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1003200 – volume: 9 start-page: e1003608 year: 2013 ident: ref61 article-title: Prediction of complex human traits using the genomic best linear unbiased predictor publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003608 – volume: 4 start-page: 270 year: 2013 ident: ref84 article-title: Evaluation of the lasso and the elastic net in genome-wide association studies publication-title: Front Genet doi: 10.3389/fgene.2013.00270 – volume: 9 start-page: 1442 year: 2012 ident: ref62 article-title: Improving the prediction of clinical outcomes from genomic data using multiresolution analysis publication-title: IEEE/ACM Trans Comput Biol Bioinform doi: 10.1109/TCBB.2012.80 – volume: 33 start-page: S51 year: 2009 ident: ref6 article-title: Machine learning in genome-wide association studies publication-title: Genet Epidemiol doi: 10.1002/gepi.20473 – volume: 27 start-page: 1 year: 2011 ident: ref111 article-title: A variable selection method for genome-wide association studies publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq600 – volume: 6 start-page: 1621 year: 2005 ident: ref97 article-title: Managing diversity in regression Ensembles publication-title: J Mach Learn Res – volume: 145 start-page: 30 year: 2011 ident: ref15 article-title: Genetic interactions in cancer progression and treatment publication-title: Cell doi: 10.1016/j.cell.2011.03.020 – volume: 20 start-page: 76 year: 2013 ident: ref39 article-title: Incremental value of rare genetic variants for the prediction of multifactorial diseases publication-title: Genome Med doi: 10.1186/gm480 – volume: 12 start-page: 2825 year: 2011 ident: ref119 article-title: Scikit-learn: machine learning in Python publication-title: J Machine Learn Res – volume: 4 start-page: 86 year: 2013 ident: ref21 article-title: Front Genet publication-title: Front Genet – volume: 10 start-page: 392 year: 2009 ident: ref17 article-title: Detecting gene-gene interactions that underlie human diseases publication-title: Nat Rev Genet doi: 10.1038/nrg2579 – volume: 7 start-page: 110 year: 2014 ident: ref96 article-title: Prediction of fetal hemoglobin in sickle cell anemia using an ensemble of genetic risk prediction models publication-title: Circ Cardiovasc Genet doi: 10.1161/CIRCGENETICS.113.000387 – volume: 26 start-page: 445 year: 2010 ident: ref7 article-title: Bioinformatics challenges for genome-wide association studies publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp713 – volume: 4 start-page: e1000130 year: 2008 ident: ref86 article-title: Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies publication-title: PLoS Genet doi: 10.1371/journal.pgen.1000130 – volume: 9 start-page: 645 year: 2013 ident: ref50 article-title: Epigenetic epistatic interactions constrain the evolution of gene expression publication-title: Mol Syst Biol doi: 10.1038/msb.2013.2 – volume: 456 start-page: 18 year: 2008 ident: ref36 article-title: Personal genomes: The case of the missing heritability publication-title: Nature doi: 10.1038/456018a – volume: 92 start-page: 1008 year: 2013 ident: ref4 article-title: Large sample size, wide variant spectrum, and advanced machine-learning technique boost risk prediction for inflammatory bowel disease publication-title: Am J Hum Genetics doi: 10.1016/j.ajhg.2013.05.002 – volume: 3 start-page: 97 year: 2012 ident: ref67 article-title: A hierarchical Bayesian approach to multi-trait clinical quantitative trait locus modeling publication-title: Front Genet doi: 10.3389/fgene.2012.00097 – volume: 13 start-page: 292 year: 2012 ident: ref92 article-title: Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations publication-title: Brief Bioinform doi: 10.1093/bib/bbr053 – volume: 45 start-page: 400 year: 2013 ident: ref31 article-title: Projecting the performance of risk prediction based on polygenic analyses of genome-wide association studies publication-title: Nat Genet doi: 10.1038/ng.2579 – volume: 42 start-page: 565 year: 2010 ident: ref34 article-title: Common SNPs explain a large proportion of the heritability for human height publication-title: Nat Genet doi: 10.1038/ng.608 – volume: 6 start-page: 6 year: 2013 ident: ref78 article-title: Using Bayesian networks to discover relations between genes, environment, and disease publication-title: BioData Min doi: 10.1186/1756-0381-6-6 – volume: 35 start-page: 111 year: 2011 ident: ref26 article-title: Mining gold dust under the genome wide significance level: a two-stage approach to analysis of GWAS publication-title: Genetic Epidemiol doi: 10.1002/gepi.20556 – volume: 188 start-page: 695 year: 2011 ident: ref112 article-title: Predicting genetic values: a kernel-based best linear unbiased prediction with genomic data publication-title: Genetics doi: 10.1534/genetics.111.128694 – volume: 85 start-page: 309 year: 2009 ident: ref14 article-title: Epistasis and its implications for personal genetics publication-title: Am J Hum Genet doi: 10.1016/j.ajhg.2009.08.006 – volume: 498 start-page: 232 year: 2013 ident: ref40 article-title: Negligible impact of rare autoimmune-locus coding-region variants on missing heritability publication-title: Nature doi: 10.1038/nature12170 – volume: 425 start-page: 3993 year: 2013 ident: ref58 article-title: Building a genome analysis pipeline to predict disease risk and prevent disease publication-title: J Mol Biol doi: 10.1016/j.jmb.2013.07.038 – volume: 7 start-page: 11 year: 2012 ident: ref30 article-title: Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations publication-title: Algorithms Mol Biol doi: 10.1186/1748-7188-7-11 – volume: 3 start-page: 176 year: 2012 ident: ref68 article-title: Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction publication-title: Front Genet doi: 10.3389/fgene.2012.00176 – volume: 376 start-page: 1393 year: 2012 ident: ref20 article-title: A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses publication-title: Lancet doi: 10.1016/S0140-6736(10)61267-6 – volume: 30 start-page: 2026 year: 2014 ident: ref71 article-title: Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu140 – volume: 37 start-page: 184 year: 2013 ident: ref24 article-title: Performance and robustness of penalized and unpenalized methods for genetic prediction of complex human disease publication-title: Genet Epidemiol doi: 10.1002/gepi.21698 – volume: 92 start-page: 744 year: 2013 ident: ref65 article-title: Genome-wide association analysis for multiple continuous secondary phenotypes publication-title: Am J Hum Genet doi: 10.1016/j.ajhg.2013.04.004 – volume: 26 start-page: 132 year: 2010 ident: ref54 article-title: Beyond genome-wide association studies: genetic heterogeneity and individual predisposition to cancer publication-title: Trends Genet doi: 10.1016/j.tig.2009.12.008 – volume: 41 start-page: 1798 year: 2012 ident: ref104 article-title: Correction for population stratification in random forest analysis publication-title: Int J Epidemiol doi: 10.1093/ije/dys183 – volume: 4 start-page: 51 year: 2013 ident: ref51 article-title: eQTL epistasis - challenges and computational approaches publication-title: Front Genet doi: 10.3389/fgene.2013.00051 – volume: 14 start-page: 483 year: 2013 ident: ref63 article-title: Pleiotropy in complex traits: challenges and strategies publication-title: Nat Rev Genet doi: 10.1038/nrg3461 – volume: 4 start-page: 138 year: 2013 ident: ref23 article-title: Evaluation of genetic risk score models in the presence of interaction and linkage disequilibrium publication-title: Front Genet – volume: 6 start-page: 5 year: 2013 ident: ref5 article-title: Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives publication-title: BioData Min doi: 10.1186/1756-0381-6-5 – volume: 28 start-page: 538 year: 2012 ident: ref56 article-title: Cancer heterogeneity: origins and implications for genetic association studies publication-title: Trends Genet doi: 10.1016/j.tig.2012.07.001 – volume: 14 start-page: 251 year: 2013 ident: ref76 article-title: Machine learning approaches for the discovery of gene-gene interactions in disease data publication-title: Brief Bioinform doi: 10.1093/bib/bbs024 – volume: 13 start-page: 135 year: 2012 ident: ref38 article-title: Rare and common variants: twenty arguments publication-title: Nat Rev Genet doi: 10.1038/nrg3118 – volume: 8 start-page: e1002822 year: 2012 ident: ref79 article-title: Chapter 11: Genome-wide association studies publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1002822 – volume: 14 start-page: 719 year: 2013 ident: ref75 article-title: Integrative approaches for finding modular structure in biological networks publication-title: Nat Rev Genet doi: 10.1038/nrg3552 – volume: 63 start-page: 1681 year: 2012 ident: ref64 article-title: Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse regression publication-title: Neuroimage doi: 10.1016/j.neuroimage.2012.08.002 – volume: 447 start-page: 661 year: 2007 ident: ref118 article-title: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls publication-title: Nature doi: 10.1038/nature05911 – volume: 14 start-page: 507 year: 2013 ident: ref28 article-title: Pitfalls of predicting complex traits from SNPs publication-title: Nat Rev Genet doi: 10.1038/nrg3457 – volume: 12 start-page: 413 year: 2013 ident: ref66 article-title: Genome-wide association studies with high-dimensional phenotypes publication-title: Stat Appl Genet Mol Biol doi: 10.1515/sagmb-2012-0032 – volume: 27 start-page: 323 year: 2011 ident: ref12 article-title: Molecular mechanisms of epistasis within and between genes publication-title: Trends Genet doi: 10.1016/j.tig.2011.05.007 – volume: 24 start-page: 1550 year: 2014 ident: ref117 article-title: MultiBLUP: improved SNP-based prediction for complex traits publication-title: Genome Res doi: 10.1101/gr.169375.113 – volume: 14 start-page: 61 year: 2013 ident: ref107 article-title: ETHNOPRED: a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-61 – volume: 7 start-page: e1002051 year: 2011 ident: ref35 article-title: Beyond missing heritability: prediction of complex traits publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002051 – volume: 82 start-page: 375 year: 2008 ident: ref110 article-title: Accommodating linkage disequilibrium in genetic-association analyses via ridge regression publication-title: Am J Hum Genet doi: 10.1016/j.ajhg.2007.10.012 – volume: 8 start-page: e1003041 year: 2012 ident: ref48 article-title: Lessons from model organisms: phenotypic robustness and missing heritability in complex disease publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003041 – volume: 29 start-page: 1086 year: 2013 ident: ref69 article-title: PleioGRiP: genetic risk prediction with pleiotropy publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt081 – volume: 13 start-page: 446 year: 2012 ident: ref74 article-title: Network biology methods integrating biological data for translational science publication-title: Brief Bioinform doi: 10.1093/bib/bbr075 – volume: 9 start-page: e93017 year: 2014 ident: ref116 article-title: Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies publication-title: PLoS ONE doi: 10.1371/journal.pone.0093017 – volume: 279 start-page: 3765 year: 2012 ident: ref46 article-title: Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience publication-title: FEBS J doi: 10.1111/j.1742-4658.2012.08810.x – volume: 9 start-page: e1003939 year: 2013 ident: ref22 article-title: Pathways-driven sparse regression identifies pathways and genes associated with high-density lipoprotein cholesterol in two Asian cohorts publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003939 – volume: 494 start-page: 234 year: 2013 ident: ref44 article-title: Finding the sources of missing heritability in a yeast cross publication-title: Nature doi: 10.1038/nature11867 – volume: 53 start-page: 23 year: 2003 ident: ref101 article-title: Theoretical and empirical analysis of ReliefF and RReliefF publication-title: Machine Learning doi: 10.1023/A:1025667309714 – volume: 131 start-page: 1639 year: 2012 ident: ref3 article-title: Risk estimation and risk prediction using machine-learning methods publication-title: Hum Genet doi: 10.1007/s00439-012-1194-y – volume: 24 start-page: 803 year: 2013 ident: ref49 article-title: Predicting phenotypic variation from genotypes, phenotypes and a combination of the two publication-title: Curr Opin Biotechnol doi: 10.1016/j.copbio.2013.03.004 – volume: 5 start-page: 60 year: 2013 ident: ref57 article-title: From personalized to public health genomics publication-title: Genome Med doi: 10.1186/gm464 – volume: 67 start-page: 301 year: 2003 ident: ref83 article-title: Regularization and variable selection via the elastic net publication-title: J Royal Stat Soc B doi: 10.1111/j.1467-9868.2005.00503.x – volume: 37 start-page: 768 year: 2013 ident: ref59 article-title: Strategies for developing prediction models from genome-wide association studies publication-title: Genet Epidemiol doi: 10.1002/gepi.21762 – volume: 28 start-page: 2086 year: 2012 ident: ref113 article-title: Synbreed: a framework for the analysis of genomic prediction data using R publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts335 – volume: 26 start-page: 2375 year: 2010 ident: ref43 article-title: Association screening of common and rare genetic variants by penalized regression publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq448 – volume: 21 start-page: 34 year: 2011 ident: ref16 article-title: Searching for synthetic lethality in cancer publication-title: Curr Opin Genet Dev doi: 10.1016/j.gde.2010.10.009 – volume: 5 start-page: e1000337 year: 2009 ident: ref27 article-title: Interpretation of genetic association studies: markers with replicated highly significant odds ratios may be poor classifiers publication-title: PLoS Genet doi: 10.1371/journal.pgen.1000337 – volume: 18 start-page: 3525 year: 2009 ident: ref25 article-title: Harnessing the information contained within genome-wide association studies to improve individual prediction of complex disease risk publication-title: Hum Mol Genet doi: 10.1093/hmg/ddp295 – volume: 46 start-page: 100 year: 2014 ident: ref106 article-title: Advantages and pitfalls in the application of mixed-model association methods publication-title: Nat Genet doi: 10.1038/ng.2876 – volume: 38 start-page: 72 year: 2014 ident: ref60 article-title: Genetic prediction of quantitative lipid traits: comparing shrinkage models to gene scores publication-title: Genet Epidemiol doi: 10.1002/gepi.21777 – volume: 9 start-page: e1003657 year: 2013 ident: ref70 article-title: GUESS-ing polygenic associations with multiple phenotypes using a GPU-based evolutionary stochastic search algorithm publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003657 – volume: 20 start-page: 1873 year: 2008 ident: ref99 article-title: Spectral algorithms for supervised learning publication-title: Neural Comput doi: 10.1162/neco.2008.05-07-517 – volume: 13 start-page: 88 year: 2012 ident: ref87 article-title: SparSNP: fast and memory-efficient analysis of all SNPs for phenotype prediction publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-13-88 – year: 2002 ident: ref98 article-title: Bagging regularizes. CBCL Memo 214 publication-title: MIT AI lab – volume: 10 start-page: 78 year: 2009 ident: ref108 article-title: Performance of random forest when SNPs are in linkage disequilibrium publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-10-78 – volume: 195 start-page: 573 year: 2013 ident: ref115 article-title: Genome-wide prediction of traits with different genetic architecture through efficient variable selection publication-title: Genetics doi: 10.1534/genetics.113.150078 – volume: 35 start-page: 506 year: 2011 ident: ref55 article-title: Evaluation of polygenic risk scores for predicting breast and prostate cancer risk publication-title: Genet Epidemiol – volume: 6 start-page: e1001146 year: 2009 ident: ref2 article-title: Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study publication-title: PLoS Genet doi: 10.1371/journal.pgen.1001146 – volume: 9 start-page: e1003348 year: 2013 ident: ref32 article-title: Power and Predictive Accuracy of Polygenic Risk Scores publication-title: PLoS Genet doi: 10.1371/journal.pgen.1003348 |
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[...]we discuss some key future advances, open questions and challenges in this developing field, when moving toward low-frequency variants and... |
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| StartPage | e1004754 |
| SubjectTerms | Artificial Intelligence Biology and Life Sciences Cardiovascular disease Computer and Information Sciences Datasets Genetic Association Studies Genetic research Genome-Wide Association Study Genomes Genotype & phenotype Health risk assessment Humans Machine learning Medicine and Health Sciences Models, Statistical Physical Sciences Quantitative trait loci Review |
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| Title | Regularized Machine Learning in the Genetic Prediction of Complex Traits |
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