Document Type

Article

Publication Date

6-22-2020

Keywords

JGM, JAXCC

JAX Source

Genome Biol 2020 Jun 22; 21(1):150

PMID

32571363

DOI

https://doi.org/10.1186/s13059-020-02033-z

Abstract

Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material. In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity. LDA(Latent Dirichlet allocation)-link connects microbes to genes using reduced-dimensionality LDA topics. We validate our method with single-cell RNA-seq and microscopy and then apply it to the sputum of asthmatic patients to find known and novel relationships between microbes and genes.

Comments

This article is licensed under a Creative Commons Attribution 4.0 International License.

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