Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test

The American Journal of Human Genetics - Tập 96 - Trang 797-807 - 2015
Ni Zhao1, Jun Chen2, Ian M. Carroll3, Tamar Ringel-Kulka4, Michael P. Epstein5, Hua Zhou6, Jin J. Zhou7, Yehuda Ringel3, Hongzhe Li8, Michael C. Wu1
1Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
2Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
3Division of Gastroenterology and Hepatology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
4Department of Maternal and Child Health, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
5Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
6Department of Statistics, North Carolina State University, Cary, Raleigh, NC 27695, USA
7Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85724, USA
8Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19014, USA

Tài liệu tham khảo

Woese, 1975, Conservation of primary structure in 16S ribosomal RNA, Nature, 254, 83, 10.1038/254083a0 Tyson, 2004, Community structure and metabolism through reconstruction of microbial genomes from the environment, Nature, 428, 37, 10.1038/nature02340 Wooley, 2010, A primer on metagenomics, PLoS Comput. Biol., 6, e1000667, 10.1371/journal.pcbi.1000667 Lasken, 2012, Genomic sequencing of uncultured microorganisms from single cells, Nat. Rev. Microbiol., 10, 631, 10.1038/nrmicro2857 Willing, 2011, Shifting the balance: antibiotic effects on host-microbiota mutualism, Nat. Rev. Microbiol., 9, 233, 10.1038/nrmicro2536 Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540 Larsen, 2010, Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults, PLoS ONE, 5, e9085, 10.1371/journal.pone.0009085 Peterson, 2008, Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases, Cell Host Microbe, 3, 417, 10.1016/j.chom.2008.05.001 Karlsson, 2013, Gut metagenome in European women with normal, impaired and diabetic glucose control, Nature, 498, 99, 10.1038/nature12198 McArdle, 2001, Fitting multivariate models to community data: a comment on distance-based redundancy analysis, Ecology, 82, 290, 10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2 Arumugam, 2011, Enterotypes of the human gut microbiome, Nature, 473, 174, 10.1038/nature09944 Lozupone, 2005, UniFrac: a new phylogenetic method for comparing microbial communities, Appl. Environ. Microbiol., 71, 8228, 10.1128/AEM.71.12.8228-8235.2005 Lozupone, 2007, Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities, Appl. Environ. Microbiol., 73, 1576, 10.1128/AEM.01996-06 Chen, 2012, Associating microbiome composition with environmental covariates using generalized UniFrac distances, Bioinformatics, 28, 2106, 10.1093/bioinformatics/bts342 Chen, 2013, Kernel Methods for Regression Analysis of Microbiome Compositional Data, 191 Kwee, 2008, A powerful and flexible multilocus association test for quantitative traits, Am. J. Hum. Genet., 82, 386, 10.1016/j.ajhg.2007.10.010 Wu, 2010, Powerful SNP-set analysis for case-control genome-wide association studies, Am. J. Hum. Genet., 86, 929, 10.1016/j.ajhg.2010.05.002 Wu, 2011, Rare-variant association testing for sequencing data with the sequence kernel association test, Am. J. Hum. Genet., 89, 82, 10.1016/j.ajhg.2011.05.029 Lee, 2012, Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies, Am. J. Hum. Genet., 91, 224, 10.1016/j.ajhg.2012.06.007 Wu, 2013, Kernel machine SNP-set testing under multiple candidate kernels, Genet. Epidemiol., 37, 267, 10.1002/gepi.21715 Chen, 2015 Goeman, 2004, A global test for groups of genes: testing association with a clinical outcome, Bioinformatics, 20, 93, 10.1093/bioinformatics/btg382 Pan, 2011, Relationship between genomic distance-based regression and kernel machine regression for multi-marker association testing, Genet. Epidemiol., 35, 211 Liu, 2007, Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models, Biometrics, 63, 1079, 10.1111/j.1541-0420.2007.00799.x Liu, 2008, Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models, BMC Bioinformatics, 9, 292, 10.1186/1471-2105-9-292 Gianola, 2008, Reproducing kernel hilbert spaces regression methods for genomic assisted prediction of quantitative traits, Genetics, 178, 2289, 10.1534/genetics.107.084285 Lin, 1997, Variance component testing in generalised linear models with random effects, Biometrika, 84, 309, 10.1093/biomet/84.2.309 Liu, 2009, A new chi-square approximation to the distribution of non-negative definite quadratic forms in non-central normal variables, Comput. Stat. Data Anal., 53, 853, 10.1016/j.csda.2008.11.025 Davies, 1980, The distribution of a linear combination of chi-2 random variables, J. R. Stat. Soc. Ser. C Appl. Stat., 29, 323 Duchesne, 2010, Computing the distribution of quadratic forms: Further comparisons between the liu-tang-zhang approximation and exact methods, Comput. Stat. Data Anal., 54, 858, 10.1016/j.csda.2009.11.025 Freedman, 1983, A nonstochastic interpretation of reported significance levels, J. Bus. Econ. Stat., 1, 292 Epstein, 2012, A permutation procedure to correct for confounders in case-control studies, including tests of rare variation, Am. J. Hum. Genet., 91, 215, 10.1016/j.ajhg.2012.06.004 Fog, 2008, Sampling methods for wallenius’ and fisher’s noncentral hypergeometric distributions, Commun. Stat. Simul. Comput., 37, 241, 10.1080/03610910701790236 Charlson, 2010, Disordered microbial communities in the upper respiratory tract of cigarette smokers, PLoS ONE, 5, e15216, 10.1371/journal.pone.0015216 Annaházi, 2009, Fecal proteases from diarrheic-IBS and ulcerative colitis patients exert opposite effect on visceral sensitivity in mice, Pain, 144, 209, 10.1016/j.pain.2009.04.017 Carroll, 2013, Fecal protease activity is associated with compositional alterations in the intestinal microbiota, PLoS ONE, 8, e78017, 10.1371/journal.pone.0078017 Crainiceanu, 2004, Likelihood ratio tests in linear mixed models with one variance component, J. R. Stat. Soc. Series B Stat. Methodol., 66, 165, 10.1111/j.1467-9868.2004.00438.x Greven, 2008, Restricted likelihood ratio testing for zero variance components in linear mixed models, J. Comput. Graph. Stat., 17, 870, 10.1198/106186008X386599 Allen, 2013, Automatic feature selection via weighted kernels and regularization, J. Comput. Graph. Stat., 22, 284, 10.1080/10618600.2012.681213