Dataset Information

Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes.

ABSTRACT:

Motivation

For many classes of disease the same genetic risk variants underly many related phenotypes or disease subtypes. Multinomial logistic regression provides an attractive framework to analyze multi-category phenotypes, and explore the genetic relationships between these phenotype categories. We introduce Trinculo, a program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association study software.

Availability and implementation

An open source C implementation, with code and binaries for Linux and Mac OSX, is available for download at http://sourceforge.net/projects/trinculo

Supplementary information

Supplementary data are available at Bioinformatics online.

Contact

lj4@well.ox.ac.uk.

SUBMITTER: Jostins L

PROVIDER: S-EPMC4908321 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes.

Jostins Luke L McVean Gilean G

Bioinformatics (Oxford, England) 20160211 12

<h4>Motivation</h4>For many classes of disease the same genetic risk variants underly many related phenotypes or disease subtypes. Multinomial logistic regression provides an attractive framework to analyze multi-category phenotypes, and explore the genetic relationships between these phenotype categories. We introduce Trinculo, a program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association s ...[more]

PMID: 26873930

Similar Datasets

Project description:BackgroundAccurate differential diagnosis of neurodegenerative parkinsonisms is challenging due to overlapping early symptoms and high rates of misdiagnosis. To improve the diagnostic accuracy, we developed an integrated classification algorithm using multinomial logistic regression and Scaled Subprofile Model/Principal Component Analysis (SSM/PCA) applied to 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) brain images. In this novel classification approach, SSM/PCA is applied to FDG-PET brain images of patients with various parkinsonisms, which are compared against the constructed undetermined images. This process involves spatial normalization of the images and dimensionality reduction via PCA. The resulting principal components are then used in a multinomial logistic regression model, which generates disease-specific topographies that can be used to classify new patients. The algorithm was trained and optimized on a cohort of patients with neurodegenerative parkinsonisms and subsequently validated on a separate cohort of patients with parkinsonisms.ResultsThe Area Under the Curve (AUC) values were the highest for progressive supranuclear palsy (PSP) (AUC = 0.95), followed by Parkinson's disease (PD) (AUC = 0.93) and multiple system atrophy (MSA) (AUC = 0.90). When classifying the patients based on their calculated probability for each group, the desired tradeoff between sensitivity and specificity had to be selected. With a 99% probability threshold for classification into a disease group, 82% of PD patients, 29% of MSA patients, and 77% of PSP patients were correctly identified. Only 5% of PD, 6% of MSA and 6% of PSP patients were misclassified, whereas the remaining patients (13% of PD, 65% of MSA and 18% of PSP) are undetermined by our classification algorithm.ConclusionsCompared to existing algorithms, this approach offers comparable accuracy and reliability in diagnosing PD, MSA, and PSP with no need of healthy control images. It can also distinguish between multiple types of parkinsonisms simultaneously and offers the flexibility to easily accommodate new groups.

Project description:ObjectivesWhether they have been engineered for it or not, most healthcare systems experience a variety of unexpected events such as appointment miss-opportunities that can have significant impact on their revenue, cost and resource utilization. In this paper, a multi-way multi-task learning model based on multinomial logistic regression is proposed to jointly predict the occurrence of different types of miss-opportunities at multiple clinics.MethodsAn extension of L1 / L2 regularization is proposed to enable transfer of information among various types of miss-opportunities as well as different clinics. A proximal algorithm is developed to transform the convex but non-smooth likelihood function of the multi-way multi-task learning model into a convex and smooth optimization problem solvable using gradient descent algorithm.ResultsA dataset of real attendance records of patients at four different clinics of a VA medical center is used to verify the performance of the proposed multi-task learning approach. Additionally, a simulation study, investigating more general data situations is provided to highlight the specific aspects of the proposed approach. Various individual and integrated multinomial logistic regression models with/without LASSO penalty along with a number of other common classification algorithms are fitted and compared against the proposed multi-way multi-task learning approach. Fivefold cross validation is used to estimate comparing models parameters and their predictive accuracy. The multi-way multi-task learning framework enables the proposed approach to achieve a considerable rate of parameter shrinkage and superior prediction accuracy across various types of miss-opportunities and clinics.ConclusionsThe proposed approach provides an integrated structure to effectively transfer knowledge among different miss-opportunities and clinics to reduce model size, increase estimation efficacy, and more importantly improve predictions results. The proposed framework can be effectively applied to medical centers with multiple clinics, especially those suffering from information scarcity on some type of disruptions and/or clinics.

Dataset Information

Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes.

Motivation

Availability and implementation

Supplementary information

Contact

Publications

Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets