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Dickson ZW, Hackenberger D, Kuch M, Marzok A, Banerjee A, Rossi L, Klowak JA, Fox-Robichaud A, Mossmann K, Miller MS, Surette MG, Golding GB, Poinar H. Probe design for simultaneous, targeted capture of diverse metagenomic targets. Cell Rep Methods 2021; 1:100069. [PMID: 35474894 PMCID: PMC9017208 DOI: 10.1016/j.crmeth.2021.100069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022]
Abstract
The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign (https://github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.
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Affiliation(s)
- Zachery W. Dickson
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Dirk Hackenberger
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Melanie Kuch
- McMaster aDNA Center, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Art Marzok
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Arinjay Banerjee
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | | | - Karen Mossmann
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Hendrik Poinar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster aDNA Center, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
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