ena-STUDY-UNIVERSITY OF EAST ANGLIA, UK-29-01-2019-18:24:20:701-8375
Simulations developed to emulate metagenomic cancer tissue sequence data.
The analysis of these metagenomes has lead to the development of SEPATH - a template computational pipeline to search for pathogens within cancer tissue sequence data. Computational tools for taxonomic classification have been reported to have widely differing levels of performance. Understanding the performance of these tools in classifying samples with low abundance bacteria and overwhelming proportions of host sequence data is a paramount step in determining the ability of these tools to accurately profile organisms within tumour sequence data. This study has simulated metagenomes based on empirical observations from cancer sequence data. These simulations are 100 different 150bp paired end metagenomes mostly comprising human reference sequence data but are impregnated with varying proportions of bacterial sequence data.   The simulations were created using BEAR from reference genomes publicly available from NCBI. For the submission of reference genomic sequence data to NCBI that were used in producing simulated metagenomes, we would like to thank and acknowledge:  - Genome Reference Consortium Human Build 38 – Genome Reference Consortium (CRG) and the International Human Genome Sequencing Consortium (IHGSC), - TIGR for the submissions of Helicobacter pylori, Haemophilus influenzae, Enterococcus faecalis, Mycoplasma genitalium - University of Wisconsin – Madison – E.coli Genome Project for their submission of E. coli - Baylor College of Medicine for their submissions of Corynebacterium accolens, Pasteurella dagmatis, Rothia dentocariosa, Streptococcus parasanguinis, Corynebacterium glucuronolyticum, Corynebacterium pseudogenitalium, Peptoniphilus duerdenii, Finegoldia magna - J. Craig Venter Institute for their submissions of Corynebacterium tuberculostearicum, Ureaplasma urealyticum, Bulleidia Extructa, Prevotella buccalis, Peptoniphilus harei, Anaerococcus prevotii, Peptoniphilus sp. BV3C26, Propionimicrobium sp. BV2F7, Anaerococcus lactolyticus, Mobiluncus curtisii, Campylobacter rectus - The Human Microbiome Project for their submission of Gemella haemolysans - Radboud University Nijmegen Medical Centre for their submission of Moraxella catarrhalis - Goettingen Genomics Laboratory for their submission of Cutibacterium acnes - The Chinese National Human Genome Centre, Shanghai for their submission of Staphylococcus epidermidis - The Department of Microbiology, University of Kaiserslautern for their submission of Streptococcus mitis - Kitasato University for their submission of Bacteroides fragilis - Washington University Genome Sequencing Center for their submissions of Abiotrophia defectiva, Cantonella morbi, Blautia hansenii, Dialister invisus, Clostridium spiroforme, Eubacterium ventriosum, Faecalibacterium prausnitzii, Ruminococcus torques, Anaerococcus Hydrogenalis - Integrated Genomics for their submission of Fusobacterium nucleatum - Washington University School of Medicine in St. Louis – McDonnel Genome Institute for their submission of Kingella oralis - DOE Joint Genome Institute for their submissions of Leptotrichia goodfellowii, Streptobacillus moniliformis, Veillonella parvula, Porphyromonas somerae, Porphyromonas bennonis, Campylobacter ureolyticus, Varibaculum cambriense, Actinotignum urinale, Propionimicrobium lymphophilum, Prevotella corporis, Anaerococcus prevotii - European Consortium for their submission of Listeria monocytogenes - Georg-August-University Goettingen, Genomic and Applied Microbiology, Goettingen Genomics Laboratory for their submission of Mannheimia haemolytica - INRS-Institut Armand Frappier for their submission of Neisseria elongate - Broad Institute for their submissions of Neisseria mucosa, Treponema Vincentii, Fusobacterium gonidiaformans, Actinobaculum massiliense, Actinomyces neuii, Actinomyces turicensis, Propionimicrobium lymphophilum, Corynebacterium pyruviciproducens  - Institut National de la Recherche Agronomique (INRA) for their submission of Streptococcus thermophilus - The Sanger Institute for their submission of Salmonella enterica - JGI for their submission of Prevotella bivia - The Genome Institute for their submission of Enterococcus faecalis - The University of Tokyo for their submission of Prevotella disiens - URMITE for their submission of Prevotella timonensis - Aalborg University for their submission of Actinotignum schaali - The Robert Koch Institute for their submission of Sneathia sanguinegens - The Genome Institute at Washington University for their submission of Peptoniphilus coxii - Institut Pasteur for their submission of Streptococcus agalactiae - University Medical Centre Utrech for their submission of Staphylococcus aureus - National Microbiology Laboratory, Public Health Agency of Canada for their submission of Streptococcus anguinosus - USDA, ARS, WRRC for their submission of Campylobacter ureolyticus   For more information please refer to the SEPATH paper (manuscript in preparation).
The analysis of these metagenomes has lead to the development of SEPATH - a template computational pipeline to search for pathogens within cancer tissue sequence data. Computational tools for taxonomic classification have been reported to have widely differing levels of performance. Understanding the performance of these tools in classifying samples with low abundance bacteria and overwhelming proportions of host sequence data is a paramount step in determining the ability of these tools to accurately profile organisms within tumour sequence data. This study has simulated metagenomes based on empirical observations from cancer sequence data. These simulations are 100 different 150bp paired end metagenomes mostly comprising human reference sequence data but are impregnated with varying proportions of bacterial sequence data.   The simulations were created using BEAR from reference genomes publicly available from NCBI. For the submission of reference genomic sequence data to NCBI that were used in producing simulated metagenomes, we would like to thank and acknowledge:  - Genome Reference Consortium Human Build 38 – Genome Reference Consortium (CRG) and the International Human Genome Sequencing Consortium (IHGSC), - TIGR for the submissions of Helicobacter pylori, Haemophilus influenzae, Enterococcus faecalis, Mycoplasma genitalium - University of Wisconsin – Madison – E.coli Genome Project for their submission of E. coli - Baylor College of Medicine for their submissions of Corynebacterium accolens, Pasteurella dagmatis, Rothia dentocariosa, Streptococcus parasanguinis, Corynebacterium glucuronolyticum, Corynebacterium pseudogenitalium, Peptoniphilus duerdenii, Finegoldia magna - J. Craig Venter Institute for their submissions of Corynebacterium tuberculostearicum, Ureaplasma urealyticum, Bulleidia Extructa, Prevotella buccalis, Peptoniphilus harei, Anaerococcus prevotii, Peptoniphilus sp. BV3C26, Propionimicrobium sp. BV2F7, Anaerococcus lactolyticus, Mobiluncus curtisii, Campylobacter rectus - The Human Microbiome Project for their submission of Gemella haemolysans - Radboud University Nijmegen Medical Centre for their submission of Moraxella catarrhalis - Goettingen Genomics Laboratory for their submission of Cutibacterium acnes - The Chinese National Human Genome Centre, Shanghai for their submission of Staphylococcus epidermidis - The Department of Microbiology, University of Kaiserslautern for their submission of Streptococcus mitis - Kitasato University for their submission of Bacteroides fragilis - Washington University Genome Sequencing Center for their submissions of Abiotrophia defectiva, Cantonella morbi, Blautia hansenii, Dialister invisus, Clostridium spiroforme, Eubacterium ventriosum, Faecalibacterium prausnitzii, Ruminococcus torques, Anaerococcus Hydrogenalis - Integrated Genomics for their submission of Fusobacterium nucleatum - Washington University School of Medicine in St. Louis – McDonnel Genome Institute for their submission of Kingella oralis - DOE Joint Genome Institute for their submissions of Leptotrichia goodfellowii, Streptobacillus moniliformis, Veillonella parvula, Porphyromonas somerae, Porphyromonas bennonis, Campylobacter ureolyticus, Varibaculum cambriense, Actinotignum urinale, Propionimicrobium lymphophilum, Prevotella corporis, Anaerococcus prevotii - European Consortium for their submission of Listeria monocytogenes - Georg-August-University Goettingen, Genomic and Applied Microbiology, Goettingen Genomics Laboratory for their submission of Mannheimia haemolytica - INRS-Institut Armand Frappier for their submission of Neisseria elongate - Broad Institute for their submissions of Neisseria mucosa, Treponema Vincentii, Fusobacterium gonidiaformans, Actinobaculum massiliense, Actinomyces neuii, Actinomyces turicensis, Propionimicrobium lymphophilum, Corynebacterium pyruviciproducens  - Institut National de la Recherche Agronomique (INRA) for their submission of Streptococcus thermophilus - The Sanger Institute for their submission of Salmonella enterica - JGI for their submission of Prevotella bivia - The Genome Institute for their submission of Enterococcus faecalis - The University of Tokyo for their submission of Prevotella disiens - URMITE for their submission of Prevotella timonensis - Aalborg University for their submission of Actinotignum schaali - The Robert Koch Institute for their submission of Sneathia sanguinegens - The Genome Institute at Washington University for their submission of Peptoniphilus coxii - Institut Pasteur for their submission of Streptococcus agalactiae - University Medical Centre Utrech for their submission of Staphylococcus aureus - National Microbiology Laboratory, Public Health Agency of Canada for their submission of Streptococcus anguinosus - USDA, ARS, WRRC for their submission of Campylobacter ureolyticus   For more information please refer to the SEPATH paper (manuscript in preparation).