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Title: Using populations of human and microbial genomes for organism detection in metagenomes

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [1] ;  [4]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Global Security Computer Applications Division
  3. Univ. of Valencia, Valencia (Spain). Inst. de Fisica Corpuscular
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Global Security Computer Applications Division
Publication Date:
OSTI Identifier:
1263571
Grant/Contract Number:
AC52-07NA27344; 33-ER-2012; 08-ER-2011
Type:
Accepted Manuscript
Journal Name:
Genome Research
Additional Journal Information:
Journal Volume: 25; Journal Issue: 7; Journal ID: ISSN 1088-9051
Publisher:
Cold Spring Harbor Laboratory Press
Research Org:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES