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MultiPhen specifications

Information


Unique identifier OMICS_04397
Name MultiPhen
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.2
Stability Stable
Requirements
MASS, abind, epitools, meta
Maintained No

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Publication for MultiPhen

MultiPhen in publications

 (15)
PMCID: 5766098
PMID: 29329304
DOI: 10.1371/journal.pone.0190788

[…] reverse regression methods take genotypes as the response variable and multiple phenotypes as predictors, such as the proportional odds logistic regression for joint model of multiple phenotypes (multiphen) []. regression approaches are able to deal with a mixture of continuous, dichotomous, and survival phenotypes, but they are complicated and few available software were developed […]

PMCID: 5717338
PMID: 29093210
DOI: 10.1098/rsob.170125

[…] any type of trait []. a limitation is the inability to adjust for covariates., another way to allow for the inclusion of traits with mixed distribution is to reverse the regression of standard gwas. multiphen performs ordinal regression of the genotype (number of minor alleles at a marker) on multiple phenotypes and tests for association using a likelihood ratio test []. alternatively, a score […]

PMCID: 5797835
PMID: 29038595
DOI: 10.1038/ng.3975

[…] does not leverage the large amount of additional phenotypic and genomic information measured in many studies. joint analyses of multiple phenotypes with each predictor of interest (e.g. manova, multiphen)– offer a gain in power, but have three major drawbacks. first, a significant result can only be interpreted as an association with any one of the phenotypes. while this is useful […]

PMCID: 5587582
PMID: 28878392
DOI: 10.1038/s41467-017-00453-3

[…] this regression model is denoted as β s. the r-squared from regressing the phenotype score on the genotype is equivalent to that from regressing the genotype on multiple phenotypes (e.g., in the multiphen method, see supplementary fig.  for equivalence of statistics). therefore, given that the joint genetic effects are homogeneous in different cohorts, the replication power using […]

PMCID: 5571642
PMID: 28836938
DOI: 10.1186/s12859-017-1791-9

[…] negative correlations between multivariate phenotypes because the situation is rare in practice. nevertheless, previous studies have demonstrated that multivariate methods such as manova [] and multiphen [] tend to have higher power to detect a pleiotropic gene in such a situation. furthermore, in this study, we only considered continuous multivariate phenotypes. future studies may extend […]


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MultiPhen institution(s)
Department of Epidemiology and Biostatistics, Imperial College London, London, UK; Department of Pediatrics, Imperial College London, London, UK; Department of Surgery and Cancer, Imperial College London, London, UK; Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand; MRC-HPA Centre for Environment and Health, Imperial College London, London, UK; Institute of Health Sciences, University of Oulu, Oulu, Finland; National Institute of Health and Welfare, Oulu, Finland; Department of Genomics of Common Disease, Imperial College London, London, UK
MultiPhen funding source(s)
Supported by the European Network for Genetic and Genomic Epidemiology Consortium (grant number P12892 DFHM), the National Institute for Health Research (NIHR) Imperial College Health Care NHS Trust Biomedical Research Centre, the European Union (grant HEALTH-2007-201550), the Academy of Finland (project grants 104781, 120315, 129269, 1114194, Center of Excellence in Complex Disease Genetics and SALVE), University Hospital Oulu, Biocenter, University of Oulu, Finland (75617), NHLBI grant 5R01HL087679-02 through the STAMPEED program (1RL1MH083268-01), NIH/NIMH (5R01MH63706:02), ENGAGE project and grant agreement HEALTH-F4-2007-201413, the Medical Research Council, UK (PrevMetSyn/SALVE) and the European Community’s Seventh Framework Programme (grant number 223367, MultiMod).

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