Metagenomic abundance estimation and diagnostic testing on species level

Nucleic Acids Research
Martin S Lindner, Bernhard Y Renard

Abstract

One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC's superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification.

References

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Citations

Feb 23, 2013·PloS One·Alexandra A-T Weber, Jan Pawlowski
Sep 11, 2013·PloS One·Thomas BonfertCaroline C Friedel
Aug 15, 2014·Nucleic Acids Research·Graham R WoodNigel Burroughs
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yu-Qing QiuShihua Zhang
Feb 3, 2015·PloS One·Martin S Lindner, Bernhard Y Renard
Mar 28, 2017·Journal of Bioinformatics and Computational Biology·Diem-Trang PhamVinhthuy Phan
Apr 20, 2017·Molecular & Cellular Proteomics : MCP·Fredrik BoulundErik Kristiansson
Jan 21, 2014·Bioinformatics·Pierre MahéJean-Baptiste Veyrieras
Mar 24, 2017·Bioinformatics·L SchaefferL Pachter
Jan 4, 2018·BMC Bioinformatics·Quang TranVinhthuy Phan
Jul 13, 2019·Nature Communications·Alexander T DiltheyAdam M Phillippy
Apr 17, 2013·Bioinformatics·Martin S LindnerBernhard Y Renard
Nov 22, 2015·Bioinformatics·Kévin VervierJean-Philippe Vert
Sep 9, 2017·Bioinformatics·Martina FischerBernhard Y Renard
Dec 18, 2020·Frontiers in Genetics·Haiyong ZhaoXiguo Yuan

Related Concepts

Taxonomy
DNA, Bacterial
Alkalescens-Dispar Group
RNA, Viral
Determination, Sequence Homology
Metagenomics
DNA
Genes
Genome
Polymerase Chain Reaction

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