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Burnham P, Gomez-Lopez N, Heyang M, Cheng AP, Lenz JS, Dadhania DM, Lee JR, Suthanthiran M, Romero R, De Vlaminck I. Separating the signal from the noise in metagenomic cell-free DNA sequencing. MICROBIOME 2020; 8:18. [PMID: 32046792 PMCID: PMC7014780 DOI: 10.1186/s40168-020-0793-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/20/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. RESULTS Here, we report low biomass background correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high-throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. CONCLUSIONS The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term. Video abstract.
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Affiliation(s)
- Philip Burnham
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Michael Heyang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Joan Sesing Lenz
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Darshana M Dadhania
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA
| | - John Richard Lee
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA
| | - Manikkam Suthanthiran
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, MD, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Epidemiology and Biostatistics, College of Human Medicine, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan Health System, Ann Arbor, MI, USA
- Detroit Medical Center, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, Florida, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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