Patents by Inventor Rigo Pantoja
Rigo Pantoja 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: 11873480Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: GrantFiled: October 16, 2015Date of Patent: January 16, 2024Assignee: ILLUMINA CAMBRIDGE LIMITEDInventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20230235395Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: ApplicationFiled: March 31, 2023Publication date: July 27, 2023Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Patent number: 11643684Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: GrantFiled: November 6, 2020Date of Patent: May 9, 2023Assignee: Illumina, Inc.Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Publication number: 20230105642Abstract: Embodiments relate to the preparation of nucleic acid libraries. Some embodiments relate to the preparation of normalized nucleic acid libraries, such as libraries in which the amounts of amplified nucleic acids are substantially the same for different amounts of input nucleic acids. Some embodiments relate to preparation of indexed nucleic acid libraries with certain adaptors.Type: ApplicationFiled: March 29, 2021Publication date: April 6, 2023Inventors: Lena Christiansen, Dmitry Pokholok, Frank J. Steemers, Rigo Pantoja, Megan Chu, Patrizia lavicoli, Weihua Chang, Jeffrey Dennis Brodin, Eric Vermaas, Jerishah Thomas, Fan Zhang
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Publication number: 20220356514Abstract: A method for detecting different analytes includes mixing different analytes with sensing probes, wherein at least some of the sensing probes are specific to respective ones of the analytes. The analytes respectively are captured by the sensing probes that are specific to those analytes. Fluorophores respectively are coupled to sensing probes that captured respective analytes. The sensing probes are mixed with beads, wherein the beads are specific to respective ones of the sensing probes, and wherein the beads include different codes identifying the analytes to which those sensing probes are specific. The sensing probes respectively are coupled to beads that are specific to those sensing probes. The beads are identified that are coupled to the sensing probes that captured analytes using at least fluorescence from the fluorophores coupled to those sensing probes. The analytes that are captured are identified.Type: ApplicationFiled: October 12, 2020Publication date: November 10, 2022Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD., ILLUMINA CAMBRIDGE LIMITEDInventors: Sarah SHULTZABERGER, Jeffrey BRODIN, Yin Nah TEO, Suzanne ROHRBACK, Rebecca MACLEOD, Rigo PANTOJA, Allen ECKHARDT, Jeffrey FISHER, Xiangyuan YANG, Kaitlin PUGLIESE, Misha GOLYNSKIY, Xiaolin WU, Seth MCDONALD
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Publication number: 20220282242Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: ApplicationFiled: April 12, 2022Publication date: September 8, 2022Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20220082569Abstract: A method is provided for detecting an element. The method includes coupling an element-sugar complex to a substrate. The element-sugar complex includes an element coupled to a sugar. The method includes coupling a lectin to the sugar; detecting the lectin; and detecting the element using at least the detection of the lectin. A system is provided that includes a substrate, and an element-sugar complex coupled to the substrate. The element-sugar complex includes an element coupled to a sugar. The system includes a lectin coupled to the sugar; and detection circuitry to detect the element using at least detection of the lectin.Type: ApplicationFiled: August 27, 2021Publication date: March 17, 2022Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.Inventors: Rigo Pantoja, Daniel Ortiz, Xiangyuan Yang, Yin Nah Teo, Eric Vermaas, Allen Eckhardt
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Patent number: 11242560Abstract: A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.Type: GrantFiled: September 10, 2018Date of Patent: February 8, 2022Assignee: Illumina, Inc.Inventors: Michael Previte, Molly He, Rigo Pantoja, Cheng-Yao Chen, Chunhong Zhou
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Publication number: 20220001384Abstract: An example of a kit includes a flow cell assembly. The flow cell assembly includes a reaction chamber, a temperature controlled flow channel in selective fluid communication with an inlet of the reaction chamber, and a filter positioned in the temperature controlled flow channel. The reaction chamber includes depressions separated by interstitial regions and capture primers attached within each of the depressions. The filter is i) to block concentrated biological sample-polymer complexes generated in the temperature controlled flow channel at a first temperature, and ii) to allow passage of concentrated biological sample and polymer released from the complexes in the temperature controlled flow channel at a second temperature.Type: ApplicationFiled: June 25, 2021Publication date: January 6, 2022Inventors: Sean M. Ramirez, Anmiv Prabhu, Rigo Pantoja, Michelle Higgins
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Publication number: 20210164040Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: ApplicationFiled: November 6, 2020Publication date: June 3, 2021Applicant: Illumina, Inc.Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Publication number: 20210130885Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: ApplicationFiled: January 11, 2021Publication date: May 6, 2021Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
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Patent number: 10913975Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: GrantFiled: July 21, 2016Date of Patent: February 9, 2021Assignee: Illumina, Inc.Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
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Patent number: 10837056Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: GrantFiled: March 13, 2019Date of Patent: November 17, 2020Assignee: Illumina, Inc.Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Patent number: 10589273Abstract: Embodiments of present application are directed to microfluidic devices and particularly digital micro-plastic fluidic devices that are specifically designed to prevent sample contamination during sample processing, methods of manufacturing the same, and methods to improve sample analysis process by preventing sample contamination.Type: GrantFiled: May 4, 2016Date of Patent: March 17, 2020Assignee: ILLUMINA, INC.Inventors: Allen E Eckhardt, Rigo Pantoja, Sean M Ramirez, Petr Capek, Edwin Li
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Publication number: 20190376136Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: ApplicationFiled: March 13, 2019Publication date: December 12, 2019Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Patent number: 10309927Abstract: Some embodiments disclosed herein provide methods of reducing reactive molecular species in a reaction carried out in a digital fluidics device having one or more electrodes by using a reaction mixture comprising an electron acceptor additive. In some embodiments, the presence of the electron acceptor additive reduces the presence of reactive molecular species in the reaction mixture. In some embodiments, the presence of the electron acceptor additive reduces the formation of gas bubbles in the digital fluidic device. Therefore, in preferred embodiments, the electron acceptor additive does not form a gas when reduced.Type: GrantFiled: April 7, 2016Date of Patent: June 4, 2019Assignee: ILLUMINA, INC.Inventors: Rigo Pantoja, Rachel M. Schowalter, Jimmy Perrott, Cyril Delattre, Allen E. Eckhardt
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Patent number: 10233493Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: GrantFiled: December 22, 2017Date of Patent: March 19, 2019Assignee: Illumina, Inc.Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Publication number: 20190048332Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: ApplicationFiled: October 29, 2018Publication date: February 14, 2019Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20190040382Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: ApplicationFiled: October 16, 2015Publication date: February 7, 2019Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20190002973Abstract: A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.Type: ApplicationFiled: September 10, 2018Publication date: January 3, 2019Applicant: Illumina, Inc.Inventors: Michael Previte, Molly He, Rigo Pantoja, Cheng-Yao Chen, Chunhong Zhou