Patents by Inventor Richard Shen
Richard Shen 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: 9453258Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.Type: GrantFiled: September 21, 2012Date of Patent: September 27, 2016Assignee: Illumina, inc.Inventors: Robert C. Kain, Xiaohai Liu, Wenyi Feng, Bernard Hirschbein, Helmy A. Eltoukhy, Xiaolin Wu, Geoffrey Paul Smith, Jonathan Mark Boutell, Thomas Joseph, Randall Smith, Min-Jui Richard Shen, Carolyn Tregidgo, Kay Klausing
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Publication number: 20160237489Abstract: Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing.Type: ApplicationFiled: March 10, 2016Publication date: August 18, 2016Applicant: Illumina, Inc.Inventors: Min-Jui Richard Shen, Robert C. Kain, Kenneth M. Kuhn, AmirAli Hajhossein Talasaz, Arash Jamshidi, George Sakaldasis, Eric Vermaas, Sebastian Bohm, Tarun Khurana, Helmy A. Eltoukhy, Jian Gong
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Patent number: 9309571Abstract: Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing.Type: GrantFiled: November 19, 2013Date of Patent: April 12, 2016Assignee: Illumina, Inc.Inventors: Min-Jui Richard Shen, Robert C. Kain, Kenneth M. Kuhn, AmirAli Hajhossein Talasaz, Arash Jamshidi, George Sakaldasis, Eric Vermaas, Sebastian Bohm, Tarun Khurana, Helmy A. Eltoukhy, Jian Gong
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Publication number: 20160053310Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: October 9, 2015Publication date: February 25, 2016Applicant: ILLUMINA, INC.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20150309058Abstract: A technique is disclosed for sample management for use in conjunction with sequencing devices that sequence biological samples, e.g., DNA and RNA. A sequencing device or a network of sequencing devices may be scheduled according to the characteristics of the samples in queue and the capabilities and availability of sequencing devices. Biological samples may be automatically queued and loaded via a sample distribution system. A sample distribution system may be used to reduce operator intervention.Type: ApplicationFiled: July 9, 2015Publication date: October 29, 2015Inventors: Robert C. Kain, Alexander G. Dickinson, Min-Jui Richard Shen, Helmy A. Eltoukhy, Francisco Jose Garcia
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Patent number: 9169513Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: October 13, 2014Date of Patent: October 27, 2015Assignee: ILLUMINA, INC.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20150259737Abstract: A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. Optionally, the polyphenolic compound is gallic acid, a lower alkyl ester thereof, or mixtures thereof. A kit includes one or more nucleotides, an enzyme capable of catalyzing incorporation of the nucleotides into a nucleic acid strand and a polyphenolic compound suitable for preparing a detection solution.Type: ApplicationFiled: June 3, 2015Publication date: September 17, 2015Applicant: Illumina, Inc.Inventors: Kay Klausing, Min-Jui Richard Shen, John Moore, Vincent Peter Smith, Kevin Hall
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Patent number: 9116139Abstract: A technique is disclosed for sample management for use in conjunction with sequencing devices that sequence biological samples, e.g., DNA and RNA. A sequencing device or a network of sequencing devices may be scheduled according to the characteristics of the samples in queue and the capabilities and availability of sequencing devices. Biological samples may be automatically queued and loaded via a sample distribution system. A sample distribution system may be used to reduce operator intervention.Type: GrantFiled: November 5, 2012Date of Patent: August 25, 2015Assignee: ILLUMINA, INC.Inventors: Robert C. Kain, Alexander G. Dickinson, Min-Jui Richard Shen, Helmy A. Eltoukhy, Francisco Jose Garcia
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Patent number: 9115353Abstract: A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. Optionally, the polyphenolic compound is gallic acid, a lower alkyl ester thereof, or mixtures thereof. A kit includes one or more nucleotides, an enzyme capable of catalyzing incorporation of the nucleotides into a nucleic acid strand and a polyphenolic compound suitable for preparing a detection solution.Type: GrantFiled: January 31, 2011Date of Patent: August 25, 2015Assignee: Illumina, Inc.Inventors: Kay Klausing, Vincent Smith, Min-Jui Richard Shen, John Moore, Kevin Hall
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Publication number: 20150232929Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.Type: ApplicationFiled: February 13, 2015Publication date: August 20, 2015Applicant: ILLUMINA, INC.Inventors: Kathryn M. Stephens, Cydne Holt, Carey Davis, Anne Jager, Paulina Walichiewicz, Yonmee Han, David Silva, Min-Jui Richard Shen, Sasan Amini, Frank J. Steemers
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Publication number: 20150203913Abstract: A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.Type: ApplicationFiled: November 13, 2014Publication date: July 23, 2015Applicant: ILLUMINA, INC.Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
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Publication number: 20150148263Abstract: The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.Type: ApplicationFiled: February 2, 2015Publication date: May 28, 2015Applicant: ILLUMINA, INC.Inventors: Andrea Sabot, Roberto Rigatti, Min-Jui Richard Shen
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Patent number: 8999642Abstract: The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.Type: GrantFiled: August 25, 2009Date of Patent: April 7, 2015Assignee: Illumina, Inc.Inventors: Andrea Sabot, Roberto Rigatti, Min-Jui Richard Shen
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Publication number: 20150080230Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: October 13, 2014Publication date: March 19, 2015Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 8906626Abstract: A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.Type: GrantFiled: September 6, 2012Date of Patent: December 9, 2014Assignee: Illumina, Inc.Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
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Patent number: 8895249Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: March 1, 2013Date of Patent: November 25, 2014Assignee: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20140329246Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimise sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimising GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilising flow cells.Type: ApplicationFiled: June 9, 2014Publication date: November 6, 2014Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen
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Publication number: 20140214579Abstract: The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and/or computing systems. In turn, the cloud computing environment may generate information for use in the cloud computing environment and/or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and/or monitoring the popularity of the sample preparation protocols.Type: ApplicationFiled: March 8, 2013Publication date: July 31, 2014Applicant: ILLUMINA, INC.Inventors: Min-Jui Richard Shen, Charles Hsuan Lin
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Patent number: 8759037Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimize sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimizing GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilizing flow cells.Type: GrantFiled: February 23, 2011Date of Patent: June 24, 2014Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen
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Publication number: 20140127792Abstract: A technique is disclosed for sample management for use in conjunction with sequencing devices that sequence biological samples, e.g., DNA and RNA. A sequencing device or a network of sequencing devices may be scheduled according to the characteristics of the samples in queue and the capabilities and availability of sequencing devices. Biological samples may be automatically queued and loaded via a sample distribution system. A sample distribution system may be used to reduce operator intervention.Type: ApplicationFiled: November 5, 2012Publication date: May 8, 2014Applicant: Illumina, Inc.Inventors: Robert C. Kain, Alexander G. Dickinson, Min-Jui Richard Shen, Helmy A. Eltoukhy, Francisco Jose Garcia