Open Access
March 2018 A phylogenetic scan test on a Dirichlet-tree multinomial model for microbiome data
Yunfan Tang, Li Ma, Dan L. Nicolae
Ann. Appl. Stat. 12(1): 1-26 (March 2018). DOI: 10.1214/17-AOAS1086


In this paper, we introduce the phylogenetic scan test (PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial (DTM) model. DTM models the microbiome data through a cascade of independent local DMs on the internal nodes of the phylogenetic tree. Each of the local DMs captures the count distributions of a certain number of operational taxonomic units at a given resolution. Since distributional differences tend to occur in clusters along evolutionary lineages, we design a scan statistic over the phylogenetic tree to allow nodes to borrow signal strength from their parents and children. We also derive a formula to bound the tail probability of the scan statistic, and verify its accuracy through simulations. The PhyloScan procedure is applied to the American Gut dataset to identify taxa associated with diet habits. Empirical studies performed on this dataset show that PhyloScan achieves higher testing power in most cases.


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Yunfan Tang. Li Ma. Dan L. Nicolae. "A phylogenetic scan test on a Dirichlet-tree multinomial model for microbiome data." Ann. Appl. Stat. 12 (1) 1 - 26, March 2018.


Received: 1 October 2016; Revised: 1 March 2017; Published: March 2018
First available in Project Euclid: 9 March 2018

zbMATH: 06894697
MathSciNet: MR3773384
Digital Object Identifier: 10.1214/17-AOAS1086

Keywords: Dirichlet-multinomial , Dirichlet-tree multinomial , microbiome , phylogenetic tree , PhyloScan , scan statistics , union probability

Rights: Copyright © 2018 Institute of Mathematical Statistics

Vol.12 • No. 1 • March 2018
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