Consistent metagenomic biomarker detection via robust PCA

Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin, Jan Suchodolski

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Recent developments of high throughput sequencing technologies allow the characterization of the microbial communities inhabiting our world. Various metagenomic studies have suggested using microbial taxa as potential biomarkers for certain diseases. In practice, the number of available samples varies from experiment to experiment. Therefore, a robust biomarker detection algorithm is needed to provide a set of potential markers irrespective of the number of available samples. Consistent performance is essential to derive solid biological conclusions and to transfer these findings into clinical applications. Surprisingly, the consistency of a metagenomic biomarker detection algorithm with respect to the variation in the experiment size has not been addressed by the current state-of-art algorithms. Results: We propose a consistency-classification framework that enables the assessment of consistency and classification performance of a biomarker discovery algorithm. This evaluation protocol is based on random resampling to mimic the variation in the experiment size. Moreover, we model the metagenomic data matrix as a superposition of two matrices. The first matrix is a low-rank matrix that models the abundance levels of the irrelevant bacteria. The second matrix is a sparse matrix that captures the abundance levels of the bacteria that are differentially abundant between different phenotypes. Then, we propose a novel Robust Principal Component Analysis (RPCA) based biomarker discovery algorithm to recover the sparse matrix. RPCA belongs to the class of multivariate feature selection methods which treat the features collectively rather than individually. This provides the proposed algorithm with an inherent ability to handle the complex microbial interactions. Comprehensive comparisons of RPCA with the state-of-the-art algorithms on two realistic datasets are conducted. Results show that RPCA consistently outperforms the other algorithms in terms of classification accuracy and reproducibility performance. Conclusions: The RPCA-based biomarker detection algorithm provides a high reproducibility performance irrespective of the complexity of the dataset or the number of selected biomarkers. Also, RPCA selects biomarkers with quite high discriminative accuracy. Thus, RPCA is a consistent and accurate tool for selecting taxanomical biomarkers for different microbial populations. Reviewers: This article was reviewed by Masanori Arita and Zoltan Gaspari.

Original languageEnglish
Article number4
JournalBiology Direct
Volume12
Issue number1
DOIs
Publication statusPublished - 31 Jan 2017
Externally publishedYes

Fingerprint

Metagenomics
Passive Cutaneous Anaphylaxis
Biomarkers
biomarker
biomarkers
Principal Component Analysis
Principal component analysis
principal component analysis
matrix
Reproducibility
Sparse matrix
reproducibility
Bacteria
Experiment
experiment
Experiments
Microbial Interactions
Low-rank Matrices
detection
bacterium

Keywords

  • Biomarker detection
  • Metagenomics
  • Robust PCA

ASJC Scopus subject areas

  • Immunology
  • Ecology, Evolution, Behavior and Systematics
  • Modelling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

Consistent metagenomic biomarker detection via robust PCA. / Alshawaqfeh, Mustafa; Bashaireh, Ahmad; Serpedin, Erchin; Suchodolski, Jan.

In: Biology Direct, Vol. 12, No. 1, 4, 31.01.2017.

Research output: Contribution to journalArticle

Alshawaqfeh, Mustafa ; Bashaireh, Ahmad ; Serpedin, Erchin ; Suchodolski, Jan. / Consistent metagenomic biomarker detection via robust PCA. In: Biology Direct. 2017 ; Vol. 12, No. 1.
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