Automated priming and library loading device
Inventors
AMINI, Sasan • Khaksar, Ramin • Taylor, Michael • Shokralla, Shadi • Haney, Christopher • Vaidyanathan, Pavan • Allred, Adam • Tran, David • Namazi, Hossein • BARSI, Julius
Assignees
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Publication Number
US-10597714-B2
Publication Date
2020-03-24
Expiration Date
Abstract
Provided herein are methods and apparatus for the identification of pathogenic and non-pathogenic microorganisms in food and environmental samples. The disclosure solves existing challenges encountered in identifying food borne pathogens, including pathogens of the Salmonella, Campylobacter, Listeria, and Escherichia genera in a timely and efficient manner. The disclosure also provides methods for differentiating a transient versus a resident pathogen, correlating presence of non-pathogenic with pathogenic microorganisms, distinguishing live versus dead microorganisms by sequencing.
Core Innovation
The invention provides a nucleic acid sequencing apparatus that includes a nucleic acid library preparation compartment operatively connected to a nucleic acid sequencing chamber. The library preparation compartment includes two or more chambers configured to prepare a plurality of nucleic acids from a sample for a sequencing reaction, and barcoded nucleic acids are generated in two or more chambers for sequencing on the same flow cell.
In the sequencing chamber, one or more flow cells are provided, each comprising a plurality of pores or sequencing cartridges configured for the passage of a nucleic acid strand. Each flow cell includes a sample input port in fluid communication with a sensing chamber outlet, where the sample input port is configured to be robotically opened and comprises a plug that projects above the surface of the flow cell for removal by a robotic tool.
An automated platform is programmed to robotically move a sample from the nucleic acid library preparation compartment into the sample input port in the nucleic acid sequencing chamber. The described system also includes indexed-barcode demultiplexing using multiple molecular indices arranged in periodic or nonperiodic block designs, including maximizing separation with defined Levenshtein distances to reduce crosstalk.
Claims Coverage
The provided content includes one independent claim defining a nucleic acid sequencing apparatus architecture with a multi-chamber library preparation compartment connected to a sequencing chamber, a robotically opened sample input port, and an automated platform for robotic transfer. The merged claim features cover four inventive features.
Library preparation compartment operatively connected to sequencing chamber
A nucleic acid library preparation compartment comprising two or more chambers configured to prepare a plurality of nucleic acids from a sample for a sequencing reaction, wherein the compartment is operatively connected to a nucleic acid sequencing chamber.
Flow cells with robotically opened sample input port and protruding plug
A nucleic acid sequencing chamber comprising one or more flow cells comprising a plurality of pores or sequencing cartridges configured for the passage of a nucleic acid strand, where each flow cell comprises a sample input port comprising a flow path in fluid communication with a sensing chamber outlet, the sample input port being configured to be robotically opened, and comprising a plug that projects a sufficient distance above the surface of the flow cell for removal by a robotic tool.
Automated platform for robotically moving the sample into the sequencing input port
An automated platform programmed to robotically move a sample from the nucleic acid library preparation compartment into the sample input port in the nucleic acid sequencing chamber.
Barcode labeling in two or more chambers
Barcodes are added to multiple nucleic acids in two or more chambers to generate barcoded nucleic acids for the sequencing reaction.
Independent claim coverage centers on an apparatus-level automation architecture linking multi-chamber library preparation to a flow-cell sequencing chamber with a robotically opened sample input port and a protruding plug, together with an automated platform programmed to robotically move the sample into the sequencing input port. Barcode labeling in two or more chambers is also recited.
Stated Advantages
Barcoded nucleic acids generated in two or more chambers are directed to sequencing on the same flow cell.
Indexed-barcode demultiplexing uses multiple molecular indices arranged in periodic or nonperiodic block designs, including maximizing separation with defined Levenshtein distances to reduce crosstalk.
A removable, projecting seal is configured so a sensor is not exposed to gas or gas-liquid interfaces and is activated by wetting and driving liquid through the device.
Cloud data analysis and supervised learning classification are described for pathogen classification.
Documented Applications
Sequencing workflows spanning pore sequencing, including ONT pore sequencing.
Related platforms, including NGS and Sanger.
Pathogen classification.
Interested in licensing this patent?