Identification of low abundance microbiome in clinical samples using whole genome sequencing
作者： Chao Zhang , Kyle Cleveland , Felice Schnoll-Sussman , Bridget McClure , Michelle Bigg
DOI: 10.1186/S13059-015-0821-Z
关键词: Helicobacter pylori 、 Microbiome 、 Microbial DNA 、 Metagenomics 、 Whole genome sequencing 、 Biology 、 Human genetics 、 International HapMap Project 、 Human genome 、 Genetics
摘要: Identifying the microbiome composition from primary tissues directly affords an opportunity to study causative relationships between host and disease. However, this is challenging due low abundance of microbial DNA relative host. We present a systematic evaluation profiling endoscopic biopsies by whole genome sequencing. compared our methods with other approaches on datasets previously identified composition. applied approach identify 27 stomach biopsies, validated presence Helicobacter pylori quantitative PCR. Finally, we profiled in The Cancer Genome Atlas gastric adenocarcinoma cohort.
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