Patents by Inventor Hongji Ren
Hongji Ren 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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Patent number: 10919033Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.Type: GrantFiled: December 17, 2018Date of Patent: February 16, 2021Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
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Patent number: 10831012Abstract: Implementations of the disclosure are directed to predicting structured illumination parameters for a particular point in time, space, and/or temperature using estimates of structured illumination parameters obtained from structured illumination images captured by a structured illumination system. Particular implementations are directed to predicting structured illumination frequency, phase, orientation, and/or modulation order parameters.Type: GrantFiled: June 20, 2019Date of Patent: November 10, 2020Assignee: ILLUMINA, INC.Inventors: Michael J. Carney, Stanley S. Hong, Robert Langlois, Hongji Ren, Kevin Wayne Bartig, Rico Otto, Olga Andreevna Souverneva
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Publication number: 20200129974Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.Type: ApplicationFiled: December 17, 2018Publication date: April 30, 2020Inventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
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Publication number: 20200004004Abstract: Implementations of the disclosure are directed to predicting structured illumination parameters for a particular point in time, space, and/or temperature using estimates of structured illumination parameters obtained from structured illumination images captured by a structured illumination system. Particular implementations are directed to predicting structured illumination frequency, phase, orientation, and/or modulation order parameters.Type: ApplicationFiled: June 20, 2019Publication date: January 2, 2020Inventors: Michael J. Carney, Stanley S. Hong, Robert Langlois, Hongji Ren, Kevin Wayne Bartig, Rico Otto, Olga Andreevna Souverneva
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Publication number: 20190233890Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: ApplicationFiled: April 10, 2019Publication date: August 1, 2019Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan Christopher Smith
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Publication number: 20190153519Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.Type: ApplicationFiled: January 18, 2019Publication date: May 23, 2019Inventors: Darren Robert Segale, John Moon, Hongji Ren
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Patent number: 10266891Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: GrantFiled: August 18, 2017Date of Patent: April 23, 2019Assignee: Illumina, Inc.Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan C. Smith
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Patent number: 10227636Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.Type: GrantFiled: January 28, 2016Date of Patent: March 12, 2019Assignee: ILLUMINA, INC.Inventors: Darren Robert Segale, John A. Moon, Hongji Ren
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Publication number: 20170342487Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: ApplicationFiled: August 18, 2017Publication date: November 30, 2017Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan C. Smith
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Patent number: 9752186Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: GrantFiled: April 6, 2015Date of Patent: September 5, 2017Assignee: Illumina, Inc.Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan C. Smith
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Publication number: 20160304940Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.Type: ApplicationFiled: January 28, 2016Publication date: October 20, 2016Applicant: Illumina, Inc.Inventors: Darren Robert Segale, John A. Moon, Hongji Ren
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Patent number: 9404737Abstract: Method of detecting surface features of a microarray. The method includes providing a microarray to an optical scanner, wherein the microarray includes a surface having features. The method also includes carrying out a scanning process using the optical scanner, wherein the scanning process includes: (i) acquiring images of sequential regions on the surface, wherein a defocus spread is applied to the optical scanner during the acquiring, (ii) determining a focus score for the images, (iii) adjusting the optical scanner to a different defocus spread based on the focus score, and (iv) repeating (i) through (iii) at the different defocus spread, thereby acquiring images of further sequential regions on the surface. The method also includes analyzing the images to distinguish different target molecules at the features of the microarray. The images that are analyzed were acquired at the defocus spread and at the different defocus spread during the scanning process.Type: GrantFiled: March 29, 2013Date of Patent: August 2, 2016Assignee: Illumina, Inc.Inventors: Darren R. Segale, John A. Moon, Hongji Ren
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Publication number: 20150259735Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: ApplicationFiled: April 6, 2015Publication date: September 17, 2015Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan C. Smith
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Patent number: 9012022Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: GrantFiled: March 4, 2013Date of Patent: April 21, 2015Assignee: Illumina, Inc.Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan C. Smith
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Publication number: 20140079923Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.Type: ApplicationFiled: March 4, 2013Publication date: March 20, 2014Inventors: Wayne N. George, Andrew A. Brown, Daniel Bratton, Hongji Ren, Ryan C. Smith
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Publication number: 20130235388Abstract: Method of detecting surface features of a microarray. The method includes providing a microarray to an optical scanner, wherein the microarray includes a surface having features. The method also includes carrying out a scanning process using the optical scanner, wherein the scanning process includes: (i) acquiring images of sequential regions on the surface, wherein a defocus spread is applied to the optical scanner during the acquiring, (ii) determining a focus score for the images, (iii) adjusting the optical scanner to a different defocus spread based on the focus score, and (iv) repeating (i) through (iii) at the different defocus spread, thereby acquiring images of further sequential regions on the surface. The method also includes analyzing the images to distinguish different target molecules at the features of the microarray. The images that are analyzed were acquired at the defocus spread and at the different defocus spread during the scanning process.Type: ApplicationFiled: March 29, 2013Publication date: September 12, 2013Applicant: ILLUMINA, INC.Inventors: Darren R. Segale, John A. Moon, Hongji Ren
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Publication number: 20110105356Abstract: Methods, kits, systems, and multilayer transfer media for transferring a substance to and from an array are disclosed herein. Also disclosed herein are methods of detecting a substance that has been transferred to an array.Type: ApplicationFiled: May 5, 2009Publication date: May 5, 2011Inventors: Chad F. DeRosier, John A. Moon, Fiona E. Black, Robert Yang, Hongji Ren, David L. Heiner
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Patent number: 7799527Abstract: The invention provides systems and methods for evaluating synthetic reactions such as polymer synthesis reactions. Evaluation of a synthetic reaction product can be based on a quantitative measure of synthesis such as coupling efficiency or yield, and various parameters determined from a separation record obtained for the synthetic reaction product. The invention further provides methods for evaluating a separation method based on various parameters determined from a separation record. The invention can be used to select an appropriate treatment for a synthetic reaction product such as a separation treatment or treatments related to further processing for the desired product. The methods are particularly useful for automated selection of treatments for synthetic reaction products.Type: GrantFiled: July 1, 2005Date of Patent: September 21, 2010Assignee: Illumina, Inc.Inventors: Nels A. Olson, Bahram Ghaffarzadeh Kermani, Hongji Ren, Theo Kotseroglou
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Publication number: 20100157086Abstract: A method and system are provided for controlling focus dynamically of a sample imager. The method comprises scanning a sample with an optical assembly that apportions the sample into regions based on a scan pattern. The optical assembly has a focal setting with respect to the sample. The method further comprises shifting the focal setting of the optical assembly during scanning of the sample, and detecting one or more images representative of one of the regions from the sample. The one or more images have associated degrees of focus corresponding to the focal setting of the optical assembly. The method analyzes the image(s) to obtain a focus score or scores corresponding thereto, where the focus scores represent a degree to which the optical assembly was in focus when detecting the images. The method adjusts the focus setting based on the focus score(s).Type: ApplicationFiled: December 15, 2009Publication date: June 24, 2010Applicant: ILLUMINA, INCInventors: DARREN R. SEGALE, JOHN A. MOON, HONGJI REN
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Publication number: 20070003941Abstract: The invention provides systems and methods for evaluating synthetic reactions such as polymer synthesis reactions. Evaluation of a synthetic reaction product can be based on a quantitative measure of synthesis such as coupling efficiency or yield, and various parameters determined from a separation record obtained for the synthetic reaction product. The invention further provides methods for evaluating a separation method based on various parameters determined from a separation record. The invention can be used to select an appropriate treatment for a synthetic reaction product such as a separation treatment or treatments related to further processing for the desired product. The methods are particularly useful for automated selection of treatments for synthetic reaction products.Type: ApplicationFiled: July 1, 2005Publication date: January 4, 2007Applicant: Illumina, Inc.Inventors: Nels Olson, Bahram Kermani, Hongji Ren, Theo Kotseroglou