Open AccessMetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers
Author(s) -
Mohamad KoohiMoghadam,
Mitesh J. Borad,
Nhan L. Tran,
Kristin R. Swanson,
Lisa A. Boardman,
Hongzhe Sun,
Junwen Wang
Publication year - 2019
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btz123
Subject(s) - metagenomics , computer science , computational biology , pipeline (software) , data mining , biology , gene , genetics , programming language
We present MetaMarker, a pipeline for discovering metagenomic biomarkers from whole-metagenome sequencing samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for CRC prediction.
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