Patents by Inventor Robert C. Kain
Robert C. Kain has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20110009296Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.Type: ApplicationFiled: September 9, 2010Publication date: January 13, 2011Applicant: ILLUMINA, INC.Inventors: Robert C. Kain, David L. Heiner, Chanfeng Zhao, Kevin Gunderson
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Publication number: 20110009278Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.Type: ApplicationFiled: September 9, 2010Publication date: January 13, 2011Applicant: ILLUMINA, INC.Inventors: Robert C. Kain, David L. Heiner, Chanfeng Zhao, Kevin Gunderson
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Patent number: 7835871Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.Type: GrantFiled: January 28, 2008Date of Patent: November 16, 2010Assignee: Illumina, Inc.Inventors: Robert C. Kain, David L. Heiner, Chanfeng Zhao, Kevin Gunderson
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Publication number: 20100137166Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.Type: ApplicationFiled: June 25, 2009Publication date: June 3, 2010Applicant: Illumina, Inc.Inventors: Robert C. Kain, David L. Heiner, Chanfeng Zhao, Kevin Gunderson
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Publication number: 20100138162Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.Type: ApplicationFiled: June 25, 2009Publication date: June 3, 2010Applicant: Illumina, Inc.Inventors: Robert C. Kain, David L. Heiner, Chanfeng Zhao, Kevin Gunderson
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Publication number: 20090298716Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.Type: ApplicationFiled: April 6, 2009Publication date: December 3, 2009Applicant: Illumina, Inc.Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
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Publication number: 20090227472Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.Type: ApplicationFiled: March 16, 2009Publication date: September 10, 2009Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
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Publication number: 20090221450Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.Type: ApplicationFiled: March 16, 2009Publication date: September 3, 2009Inventors: John R Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
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Publication number: 20090215649Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.Type: ApplicationFiled: March 16, 2009Publication date: August 27, 2009Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
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Publication number: 20080262747Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.Type: ApplicationFiled: January 28, 2008Publication date: October 23, 2008Applicant: Illumina, Inc.Inventors: Robert C. Kain, David L. Heiner, Chanfeng Zhao, Kevin Gunderson
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Publication number: 20080182757Abstract: A technique is disclosed for performing sequencing of polymers such as DNA and RNA. A sample containing multiple sites to be sequenced is cyclically subjected to attachment of nucleotides, and imaging. A digital mask corresponding to sites of interest in the sample array is generated and image data for the sites is processed differently from image data not corresponding to sites of interest. The latter may be discarded during the sequencing operation. The use of the mask improves computational efficiency and reduces memory allocated for the image data during sequencing.Type: ApplicationFiled: January 28, 2008Publication date: July 31, 2008Applicant: Illumina, Inc.Inventors: David L. Heiner, Robert C. Kain
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Publication number: 20040185482Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.Type: ApplicationFiled: January 28, 2004Publication date: September 23, 2004Applicant: Illumina, Inc.Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
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Patent number: 6177990Abstract: A sample substrate for use in a fluorescence imaging system includes a rigid base with a specularly reflective surface, typically metal, on which is deposited a transparent coating layer. The coating layer has a thickness selected so that a particular fluorescence excitation wavelength, corresponding to a specified fluorescent constituent to be sought in sample material, has an optical path from the top of the coating layer to the reflecting surface in the base of substantially an odd multiple of one-quarter wavelength, so that the standing wave of the fluorescence excitation wavelength of light incident on the substrate has an antinode located at or near where sample material would be disposed on top of the coating layer. This maximizes fluorescence excitation of the sample on the reflective substrate. The transparent coating layer may be a dielectric material (e.g. silica) or may be a multilayer structure with a top layer of biologically active material for binding a specified sample constituent.Type: GrantFiled: December 21, 1999Date of Patent: January 23, 2001Assignee: Molecular Dynamics, Inc.Inventors: Robert C. Kain, Eric G. Marason, Richard F. Johnston
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Patent number: 6008892Abstract: A sample substrate for use in a fluorescence imaging system includes a rigid base with a specularly reflective surface, typically metal, on which is deposited a transparent coating layer. The coating layer has a thickness selected so that a particular fluorescence excitation wavelength, corresponding to a specified fluorescent constituent to be sought in sample material, has an optical path from the top of the coating layer to the reflecting surface in the base of substantially an odd multiple of one-quarter wavelength, so that the standing wave of the fluorescence excitation wavelength of light incident on the substrate has an antinode located at or near where sample material would be disposed on top of the coating layer. This maximizes fluorescence excitation of the sample on the reflective substrate. The transparent coating layer may be a dielectric material (e.g. silica) or may be a multilayer structure with a top layer of biologically active material for binding a specified sample constituent.Type: GrantFiled: May 23, 1997Date of Patent: December 28, 1999Assignee: Molecular Dynamics, Inc.Inventors: Robert C. Kain, Eric G. Marason, Richard F. Johnston
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Patent number: 5847400Abstract: A coaxial illumination and collection laser scanning system designed to provide increased sensitivity by reducing auto-fluorescence while having a substantially uniform detection sensitivity across the field of view of an objective lens by reducing lateral chromatic aberrations at the expense of amplifying axial chromatic aberrations. Axial chromatic aberrations in the system are removed in the path of a retro-beam. A laser is in optical communication with the objective lens. The laser produces a collimated beam of coherent light that is directed by a scanner through the objective lens to illuminate a raster of spots on the sample's surface, thereby stimulating a series of small regions of the sample to emit light. The system may be used as a confocal or non-confocal imaging system.Type: GrantFiled: January 30, 1997Date of Patent: December 8, 1998Assignee: Molecular Dynamics, Inc.Inventors: Robert C. Kain, Christopher C. Alexay
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Patent number: 5754291Abstract: The present invention features two flat-field, telecentric, infinite conjugate, achromatic objectives each of which has an external pupil lying in a common plane located equidistant from the two objectives, defining a mechanically accessible central pupil of an imaging system centered in the common plane. Each of the objectives are afocal in the common plane, with one of the lenses forming a focal plane proximate to a sample. The lenses are adapted to provide varying levels of magnification while keeping constant the number of resolvable points in the field of view. An array detector is positioned proximate to a focal plane formed of the remaining objective lens. The double objective lens assembly is described as being included in transillumination and epi-illumination systems.Type: GrantFiled: September 19, 1996Date of Patent: May 19, 1998Assignee: Molecular Dynamics, Inc.Inventor: Robert C. Kain
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Patent number: 5719391Abstract: A fluorescence imaging system that includes an objective that is both achromatic and has an external entrance pupil. The objective also serves as a condenser for the system which substantially reduces the system's cost and footprint. With the objective positioned above a sample so that they are in close proximity to one another, a laser directs a collimated beam of light to a scan device located at the objective entrance pupil. The scan device reflects, refracts, or diffracts the light through the lens to illuminate a spot on the sample's surface. The scan device illuminates a line or an area on the sample surface by varying the angle of laser light, in one or two dimensions, into the objective. The sample emits fluorescent light in response to the illumination. The fluorescence light is collected by the objective and passes through the system along the path of the illumination light.Type: GrantFiled: March 15, 1996Date of Patent: February 17, 1998Assignee: Molecular Dynamics, Inc.Inventor: Robert C. Kain
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Patent number: 5672880Abstract: A fluorescence imaging system that includes an objective that is both achromatic and has an external entrance pupil. The objective also serves as a condenser for the system which substantially reduces the system's cost and footprint. With the objective positioned above a sample so that they are in close proximity to one another, a laser directs a collimated beam of light to a scan device located at the objective entrance pupil. The scan device reflects, refracts, or diffracts the light through the lens to illuminate a spot on the sample's surface. The scan device illuminates a line or an area on the sample surface by varying the angle of laser light, in one or two dimensions, into the objective. The sample emits fluorescent light in response to the illumination. The fluorescence light is collected by the objective and passes through the system along the path of the illumination light.Type: GrantFiled: March 15, 1996Date of Patent: September 30, 1997Assignee: Molecular Dynamics, Inc.Inventor: Robert C. Kain
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Patent number: 5646411Abstract: A coaxial illumination and collection laser scanning system provides substantially uniform detection sensitivity across the field of view of an objective lens by reducing lateral chromatic aberrations at the expense of amplifying axial chromatic aberrations. Axial chromatic aberrations in the system are removed in the path of a retro-beam. A laser is in optical communication with the objective lens. The laser produces a collimated beam of coherent light that is directed by a scanner through the objective lens to illuminate a raster of spots on the sample's surface, thereby stimulating a series of small regions of the sample to emit light. The system may be used as a confocal or non-confocal imaging system. Alternatively, the system may be employed for reflection imaging of the laser beam. In a second embodiment, a plurality of lasers are provided, each of which emits a wavelength different from the remaining lasers.Type: GrantFiled: February 1, 1996Date of Patent: July 8, 1997Assignee: Molecular Dynamics, Inc.Inventors: Robert C. Kain, Christopher C. Alexay
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Patent number: 5578818Abstract: An LED point imaging scanner for stimulating and for reading fluorescent and reflective signal radiation from a target sample is disclosed. The LED light source is mounted on a scan head and is focused into the pinhole aperture of a spatial filter, then collimated and focused to a spot on the sample. The spatial filter in the illumination path, or an optical fiber serving the equivalent function, effectively restricts the incoherent LED light and creates a point light source. Signal radiation from the sample is collected through the scan head and the returning light beam is collimated and focused onto the receiving section of a detection means. A spatial filter in the path of the returning beam may also be utilized. The detection means is either a small detector which is mounted directly on the scan head or an end of an optical fiber which transmits the point image to a remotely-positioned stationary detector.Type: GrantFiled: May 10, 1995Date of Patent: November 26, 1996Assignee: Molecular DynamicsInventors: Robert C. Kain, Michael F. Miller, Lars Majlof