Quantitative detection of pathogens in centrifugal microfluidic disks

Koh, Chung-Yan; Schaff, Ulrich Y.; Sommer, Gregory Jon

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Title: Quantitative detection of pathogens in centrifugal microfluidic disks

Abstract

A system and methods for detection of a nucleic acid including forming a plurality of nucleic acid detection complexes are described, each of the complexes including a nucleic acid analyte, a detection agent and a functionalized probe. The method further including binding the nucleic acid detection complexes to a plurality of functionalized particles in a fluid sample and separating the functionalized particles having the nucleic acid detection complexes bound thereto from the fluid sample using a density media. The nucleic acid analyte is detected by detecting the detection agent.

Inventors:: Koh, Chung-Yan; Schaff, Ulrich Y.; Sommer, Gregory Jon

Issue Date:: 2018-02-27

Research Org.:: Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1423444

Patent Number(s):: 9903001

Application Number:: 13/941,186

Assignee:: National Technology & Engineering Solutions of Sandia, LLC (Albuquerque, NM)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q1/6818 - involving interaction of two or more labels, e.g. resonant energy transfer
C12Q1/689 - for bacteria
C12Q2565/629 - being a microfluidic device

Show less

DOE Contract Number:: AC04-94AL85000

Resource Type:: Patent

Resource Relation:: Patent File Date: 2013 Jul 12

Country of Publication:: United States

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES

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                    Koh, Chung-Yan, Schaff, Ulrich Y., and Sommer, Gregory Jon. Quantitative detection of pathogens in centrifugal microfluidic disks.  United States: N. p., 2018. 
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                    Koh, Chung-Yan, Schaff, Ulrich Y., & Sommer, Gregory Jon. Quantitative detection of pathogens in centrifugal microfluidic disks.  United States.

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                    Koh, Chung-Yan, Schaff, Ulrich Y., and Sommer, Gregory Jon. Tue .  
        "Quantitative detection of pathogens in centrifugal microfluidic disks".  United States.  https://www.osti.gov/servlets/purl/1423444.

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@article{osti_1423444,

  title        = {Quantitative detection of pathogens in centrifugal microfluidic disks},

  author       = {Koh, Chung-Yan and Schaff, Ulrich Y. and Sommer, Gregory Jon},

  abstractNote = {A system and methods for detection of a nucleic acid including forming a plurality of nucleic acid detection complexes are described, each of the complexes including a nucleic acid analyte, a detection agent and a functionalized probe. The method further including binding the nucleic acid detection complexes to a plurality of functionalized particles in a fluid sample and separating the functionalized particles having the nucleic acid detection complexes bound thereto from the fluid sample using a density media. The nucleic acid analyte is detected by detecting the detection agent.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2018},

  month        = {2}

}

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URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20050215410

Method and Apparatus For Precise Transfer and Manipulation Of Fluids By Centrifugal and Or Capillary Forces
patent-application, January 2009

Pugia, Michael J.; Blankenstein, Gert; Peters, Ralf-Peter
US Patent Document 12/205965; 20090004059
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20090004059

A rapid direct fluorescent assay for cell-free DNA quantification in biological fluids
journal, September 2009

Goldshtein, H.; Hausmann, M. J; Douvdevani, A.
Annals of Clinical Biochemistry, Vol. 46, Issue 6, p. 488-494
https://doi.org/10.1258/acb.2009.009002

Molecular Detection of Bacterial Pathogens Using Microparticle Enhanced Double-Stranded DNA Probes
journal, August 2011

Riahi, Reza; Mach, Kathleen E.; Mohan, Ruchika
Analytical Chemistry, Vol. 83, Issue 16, p. 6349-6354
https://doi.org/10.1021/ac2012575

Assay system and method for conducting assays
patent, March 1999

Andrevski, Zygmunt M.; Roach, William R.; Southgate, Peter D.
US Patent Document 5,882,903
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5882903

Circulating DNA: a new diagnostic gold mine?
journal, October 2002

Ziegler, Annemarie; Zangemeister-Wittke, Uwe; Stahel, Rolf A.
Cancer Treatment Reviews, Vol. 28, Issue 5, p. 255-271
https://doi.org/10.1016/S0305-7372(02)00077-4

Compact disk based platform for separating and detecting immunomagnetic bead labeled cells
patent-application, June 2010

Wo, Andrew M.; Chen, Chen-Lin; Chen, Ken-Chao
US Patent Application12/382844; 20100151560
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20100151560

Lab On A CD
journal, August 2006

Madou, Marc; Zoval, Jim; Jia, Guangyao
Annual Review of Biomedical Engineering, Vol. 8, Issue 1, p. 601-628
https://doi.org/10.1146/annurev.bioeng.8.061505.095758

Apparatus and method for measuring white blood cell and platelet concentrations in blood
patent, May 1979

Wardlaw, Stephen C.
US Patent Document 4,156,570
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/4156570

Multi-parameter assays including analysis discs and methods relating thereto
patent, April 2006

Gordon, John Francis
US Patent Document 7,033,747
URL: https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/7033747

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Title: Quantitative detection of pathogens in centrifugal microfluidic disks

Abstract

Citation Formats

Method for separating the cellular components of blood samples patent, July 1989

Density-based cell detection system patent, March 2010

Capillary columns with in situ formed porous monolithic packing for micro high-performance liquid chromatography and capillary electrochromatography journal, September 1999

Devices and Method For Using Centripetal Acceleration To Drive Fluid Movement In A Microfluidics System With On-Board Informatics patent-application, December 2001

Assay of blood or other biologic samples for target analytes patent, June 1997

Systems and Methods for Handling Microfluidic Droplets patent-application, October 2013

Diagnostic tests and kits for Clostridium difficile patent, January 2003

Optical bio-discs and fluidic circuits for analysis of cells and methods relating thereto patent, January 2007

Centrifugal force based microfluidic device, microfluidic system including the same, and method of determining home position of the microfluidic device patent, July 2010

Analytical methods and compositions patent-application, November 2002

Separation Device patent-application, May 2010

Loading Disk for Photometric Analyzer of Rotary Cuvette Type patent, July 1973

Portable Simultaneous Multiple Analyte Whole-Blood Analyzer for Point-of-Care Testing journal, September 1992

Class characterization of circulating cancer cells isolated from body fluids and methods of use patent-application, July 2002

Method for separating cells patent-application, July 2003

Cell-Free Plasma DNA as a Predictor of Outcome in Severe Sepsis and Septic Shock journal, April 2008

Shiga toxin 1 acting on DNA in vitro is a heat-stable enzyme not requiring proteolytic activation journal, April 2004

Polyethyleneimine functionalized iron oxide nanoparticles as agents for DNA delivery and transfection journal, January 2007

Multi-parameter assays including analysis discs and methods relating thereto patent-application, October 2002

Centrifugal Separation System patent-application, August 2009

Protecting agent patent-application, August 2005

Apparatus and method for carrying out analysis of samples patent, April 1999

Staphylococcal Enterotoxin B as a Biological Weapon: Recognition, Management, and Surveillance of Staphylococcal Enterotoxin journal, September 2006

Micro freef-low IEF enhanced by active cooling and functionalized gels journal, December 2006

Depurination of A4256 in 28 S rRNA by the Ribosome-inactivating Proteins from Barley and Ricin Results in Different Ribosome Conformations journal, May 1996

Centrifugation Apparatus For Containers Of Biological Material patent-application, February 2011

Ricin A-Chain Activity on Stem−Loop and Unstructured DNA Substrates journal, March 2005

Measurement of Circulating Cell-Free DNA Levels by a New Simple Fluorescent Test in Patients With Primary Colorectal Cancer journal, February 2011

Method For Isolating Nucleic Acids Comprising The Use Of Ethylene Glycol Multimers patent-application, March 2009

A molecular approach to bioseparations: Protein–protein and protein–salt interactions journal, February 2006

Method and apparatus for measuring blood constituent counts patent, July 1987

Parallel Nanoliter Microfluidic Analysis System journal, June 2007

Functional integration of DNA purification and concentration into a real time micro-PCR chip journal, January 2011

Multistation, Single Channel Analytical Photometer and Method of Use patent, January 1971

Method and apparatus for fully automated nucleic acid amplification, nucleic acid assay and immunoassay patent, June 1997

Separation of solid and liquid components of mixtures patent, November 1978

Whole Blood Immunoassay Based on Centrifugal Bead Sedimentation journal, March 2011

Diagnostic Analyzers With Pretreatment Carousels and Related Methods patent-application, September 2014

Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function journal, June 2011

Read-out concepts for multiplexed bead-based fluorescence immunoassays on centrifugal microfluidic platforms journal, February 2006

Characterization of EBV-genome negative “null” and “T” cell lines derived from children with acute lymphoblastic leukemia and leukemic transformed non-Hodgkin lymphoma journal, May 1977

Monolithic microfluidic concentrators and mixers patent, May 2005

Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays journal, January 2007

Centripetally-motivated microfluidics system for performing in vitro hybridization and amplification of nucleic acids patent, February 2008

Microparticle-based methods and systems and applications thereof patent-application, December 2005

Comparison of sample fixation and the use of LDS-751 or anti-CD45 for leukocyte identification in mouse whole blood for flow cytometry journal, January 2007

Microfluidic particle-analysis systems patent-application, April 2004

Centrifugal Microfluidic Platform for Ultrasensitive Detection of Botulinum Toxin journal, December 2014

A B Cell-Based Sensor for Rapid Identification of Pathogens journal, July 2003

Cell-Free DNA—A Marker to Predict Ischemic Brain Damage in a Rat Stroke Experimental Model journal, January 2011

Heterogeneous binding assay patent, April 1987

DNA purification and isolation using magnetic particles patent, January 1998

Detection of Listeria monocytogenes and the toxin listeriolysin O in food journal, February 2006

A new biodosimetric method: branched DNA-based quantitative detection of B1 DNA in mouse plasma journal, August 2010

Leukocyte analysis and differentiation using high speed microfluidic single cell impedance cytometry journal, January 2009

Centrifugal hematology disposable patent, November 2000

Reagents for labeling biomolecules having aldehyde or ketone Moieties patent-application, September 2002

Bead-based microfluidic immunoassays: The next generation journal, February 2007

Method for detecting analytes in a sample patent-application, December 2009

Photopolymerized diffusion-defined polyacrylamide gradient gels for on-chip protein sizing journal, January 2008

Infrared controlled waxes for liquid handling and storage on a CD-microfluidic platform journal, January 2011

Devices and methods for using centripetal acceleration to drive fluid movement in a microfluidics system patent, November 2001

Method of separation employing magnetic particles and second medium patent, January 1994

Quantitative Comparison of Long-wavelength Alexa Fluor Dyes to Cy Dyes: Fluorescence of the Dyes and Their Bioconjugates journal, December 2003

Fully Integrated Lab-on-a-Disc for Nucleic Acid Analysis of Food-Borne Pathogens journal, March 2014

Plasma DNA as a Prognostic Marker in Trauma Patients journal, March 2000

Fully integrated lab-on-a-disc for simultaneous analysis of biochemistry and immunoassay from whole blood journal, January 2011

Microfluidics devices and methods for performing cell based assays patent-application, August 2002

Design Strategies and Performance of Custom DNA Sequencing Primers journal, September 1999

Centrifuge with removable core for scalable centrifugation patent-application, September 2005

Method and Apparatus For Precise Transfer and Manipulation Of Fluids By Centrifugal and Or Capillary Forces patent-application, January 2009

A rapid direct fluorescent assay for cell-free DNA quantification in biological fluids journal, September 2009

Molecular Detection of Bacterial Pathogens Using Microparticle Enhanced Double-Stranded DNA Probes journal, August 2011

Assay system and method for conducting assays patent, March 1999

Circulating DNA: a new diagnostic gold mine? journal, October 2002

Compact disk based platform for separating and detecting immunomagnetic bead labeled cells patent-application, June 2010

Lab On A CD journal, August 2006

Method for separating the cellular components of blood samples
patent, July 1989

Density-based cell detection system
patent, March 2010

Capillary columns with in situ formed porous monolithic packing for micro high-performance liquid chromatography and capillary electrochromatography
journal, September 1999

Devices and Method For Using Centripetal Acceleration To Drive Fluid Movement In A Microfluidics System With On-Board Informatics
patent-application, December 2001

Assay of blood or other biologic samples for target analytes
patent, June 1997

Systems and Methods for Handling Microfluidic Droplets
patent-application, October 2013

Diagnostic tests and kits for Clostridium difficile
patent, January 2003

Optical bio-discs and fluidic circuits for analysis of cells and methods relating thereto
patent, January 2007

Centrifugal force based microfluidic device, microfluidic system including the same, and method of determining home position of the microfluidic device
patent, July 2010

Analytical methods and compositions
patent-application, November 2002

Separation Device
patent-application, May 2010

Loading Disk for Photometric Analyzer of Rotary Cuvette Type
patent, July 1973

Portable Simultaneous Multiple Analyte Whole-Blood Analyzer for Point-of-Care Testing
journal, September 1992

Class characterization of circulating cancer cells isolated from body fluids and methods of use
patent-application, July 2002

Method for separating cells
patent-application, July 2003

Cell-Free Plasma DNA as a Predictor of Outcome in Severe Sepsis and Septic Shock
journal, April 2008

Shiga toxin 1 acting on DNA in vitro is a heat-stable enzyme not requiring proteolytic activation
journal, April 2004

Polyethyleneimine functionalized iron oxide nanoparticles as agents for DNA delivery and transfection
journal, January 2007

Multi-parameter assays including analysis discs and methods relating thereto
patent-application, October 2002

Centrifugal Separation System
patent-application, August 2009

Protecting agent
patent-application, August 2005

Apparatus and method for carrying out analysis of samples
patent, April 1999

Staphylococcal Enterotoxin B as a Biological Weapon: Recognition, Management, and Surveillance of Staphylococcal Enterotoxin
journal, September 2006

Micro freef-low IEF enhanced by active cooling and functionalized gels
journal, December 2006

Depurination of A4256 in 28 S rRNA by the Ribosome-inactivating Proteins from Barley and Ricin Results in Different Ribosome Conformations
journal, May 1996

Centrifugation Apparatus For Containers Of Biological Material
patent-application, February 2011

Ricin A-Chain Activity on Stem−Loop and Unstructured DNA Substrates
journal, March 2005

Measurement of Circulating Cell-Free DNA Levels by a New Simple Fluorescent Test in Patients With Primary Colorectal Cancer
journal, February 2011

Method For Isolating Nucleic Acids Comprising The Use Of Ethylene Glycol Multimers
patent-application, March 2009

A molecular approach to bioseparations: Protein–protein and protein–salt interactions
journal, February 2006

Method and apparatus for measuring blood constituent counts
patent, July 1987

Parallel Nanoliter Microfluidic Analysis System
journal, June 2007

Functional integration of DNA purification and concentration into a real time micro-PCR chip
journal, January 2011

Multistation, Single Channel Analytical Photometer and Method of Use
patent, January 1971

Method and apparatus for fully automated nucleic acid amplification, nucleic acid assay and immunoassay
patent, June 1997

Separation of solid and liquid components of mixtures
patent, November 1978

Whole Blood Immunoassay Based on Centrifugal Bead Sedimentation
journal, March 2011

Diagnostic Analyzers With Pretreatment Carousels and Related Methods
patent-application, September 2014

Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function
journal, June 2011

Read-out concepts for multiplexed bead-based fluorescence immunoassays on centrifugal microfluidic platforms
journal, February 2006

Characterization of EBV-genome negative “null” and “T” cell lines derived from children with acute lymphoblastic leukemia and leukemic transformed non-Hodgkin lymphoma
journal, May 1977

Monolithic microfluidic concentrators and mixers
patent, May 2005

Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays
journal, January 2007

Centripetally-motivated microfluidics system for performing in vitro hybridization and amplification of nucleic acids
patent, February 2008

Microparticle-based methods and systems and applications thereof
patent-application, December 2005

Comparison of sample fixation and the use of LDS-751 or anti-CD45 for leukocyte identification in mouse whole blood for flow cytometry
journal, January 2007

Microfluidic particle-analysis systems
patent-application, April 2004

Centrifugal Microfluidic Platform for Ultrasensitive Detection of Botulinum Toxin
journal, December 2014

A B Cell-Based Sensor for Rapid Identification of Pathogens
journal, July 2003

Cell-Free DNA—A Marker to Predict Ischemic Brain Damage in a Rat Stroke Experimental Model
journal, January 2011

Heterogeneous binding assay
patent, April 1987

DNA purification and isolation using magnetic particles
patent, January 1998

Detection of Listeria monocytogenes and the toxin listeriolysin O in food
journal, February 2006

A new biodosimetric method: branched DNA-based quantitative detection of B1 DNA in mouse plasma
journal, August 2010

Leukocyte analysis and differentiation using high speed microfluidic single cell impedance cytometry
journal, January 2009

Centrifugal hematology disposable
patent, November 2000

Reagents for labeling biomolecules having aldehyde or ketone Moieties
patent-application, September 2002

Bead-based microfluidic immunoassays: The next generation
journal, February 2007

Method for detecting analytes in a sample
patent-application, December 2009

Photopolymerized diffusion-defined polyacrylamide gradient gels for on-chip protein sizing
journal, January 2008

Infrared controlled waxes for liquid handling and storage on a CD-microfluidic platform
journal, January 2011

Devices and methods for using centripetal acceleration to drive fluid movement in a microfluidics system
patent, November 2001

Method of separation employing magnetic particles and second medium
patent, January 1994

Quantitative Comparison of Long-wavelength Alexa Fluor Dyes to Cy Dyes: Fluorescence of the Dyes and Their Bioconjugates
journal, December 2003

Fully Integrated Lab-on-a-Disc for Nucleic Acid Analysis of Food-Borne Pathogens
journal, March 2014

Plasma DNA as a Prognostic Marker in Trauma Patients
journal, March 2000

Fully integrated lab-on-a-disc for simultaneous analysis of biochemistry and immunoassay from whole blood
journal, January 2011

Microfluidics devices and methods for performing cell based assays
patent-application, August 2002

Design Strategies and Performance of Custom DNA Sequencing Primers
journal, September 1999

Centrifuge with removable core for scalable centrifugation
patent-application, September 2005

Method and Apparatus For Precise Transfer and Manipulation Of Fluids By Centrifugal and Or Capillary Forces
patent-application, January 2009

A rapid direct fluorescent assay for cell-free DNA quantification in biological fluids
journal, September 2009

Molecular Detection of Bacterial Pathogens Using Microparticle Enhanced Double-Stranded DNA Probes
journal, August 2011

Assay system and method for conducting assays
patent, March 1999

Circulating DNA: a new diagnostic gold mine?
journal, October 2002

Compact disk based platform for separating and detecting immunomagnetic bead labeled cells
patent-application, June 2010

Lab On A CD
journal, August 2006

Apparatus and method for measuring white blood cell and platelet concentrations in blood
patent, May 1979

Multi-parameter assays including analysis discs and methods relating thereto
patent, April 2006