Patents by Inventor Joakim Lundeberg

Joakim Lundeberg 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).

  • Publication number: 20220298560
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: June 7, 2022
    Publication date: September 22, 2022
    Applicants: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 11390912
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Grant
    Filed: March 11, 2022
    Date of Patent: July 19, 2022
    Assignees: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Publication number: 20220213526
    Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.
    Type: Application
    Filed: March 25, 2022
    Publication date: July 7, 2022
    Applicant: Spatial Transcriptomics AB
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg
  • Publication number: 20220195505
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: March 11, 2022
    Publication date: June 23, 2022
    Applicants: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 11352659
    Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.
    Type: Grant
    Filed: September 14, 2021
    Date of Patent: June 7, 2022
    Assignee: Spatial Transcriptomics AB
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg
  • Publication number: 20220127659
    Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.
    Type: Application
    Filed: September 14, 2021
    Publication date: April 28, 2022
    Applicant: Spatial Transcriptomics AB
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg
  • Patent number: 11299774
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Grant
    Filed: September 20, 2021
    Date of Patent: April 12, 2022
    Assignees: Spatial Transcriptomics AB, Illumina Inc
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Publication number: 20220106633
    Abstract: Provided herein are methods, compositions, and kits for the detection of immune cell clonotypes and immune cell analytes within a biological sample.
    Type: Application
    Filed: December 15, 2021
    Publication date: April 7, 2022
    Inventors: Camilla Engblom, Kim Thrane, Jeffrey Mold, Jonas Frisen, Joakim Lundeberg, Qirong Lin
  • Publication number: 20220090058
    Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.
    Type: Application
    Filed: September 14, 2021
    Publication date: March 24, 2022
    Applicant: Spatial Transcriptomics AB
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg
  • Publication number: 20220049293
    Abstract: Provided herein are methods of determining a location of a biological analyte in a biological sample.
    Type: Application
    Filed: December 6, 2019
    Publication date: February 17, 2022
    Applicant: 10x Genomics, Inc.
    Inventors: Lucas Frenz, Eswar Prasad Ramachandran Iyer, Tarjei Sigurd Mikkelsen, Preyas Shah, Katherine Pfeiffer, Yifeng Yin, Elliott Meer, Jessica Michele Terry, Yi Luo, Shalini Gohil, Joshua Delaney, Adam Lowe, Linda Kvastad, Eva Gracia Villacampa, Ludvig Larsson, Joakim Lundeberg, Zachary Bent, Meghan L. F. Frey, Jennifer Chew
  • Publication number: 20220049294
    Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.
    Type: Application
    Filed: December 6, 2019
    Publication date: February 17, 2022
    Applicant: 10x Genomics, Inc.
    Inventors: Cedric Uytingco, Zachary Bent, Eswar Prasad Ramachandran Iyer, Fernandino Valdecanas, Meghan L. F. Frey, Steven William Short, Yifeng Yin, Augusto Manuel Tentori, Rajiv Bharadwaj, David Maurice Cox, Jennifer Chew, Joakim Lundeberg, Felice Alessio Bava, Linda Kvastad, Andrew D. Price
  • Publication number: 20220002791
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: September 20, 2021
    Publication date: January 6, 2022
    Applicants: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 11162132
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Grant
    Filed: April 22, 2021
    Date of Patent: November 2, 2021
    Assignees: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Publication number: 20210324457
    Abstract: This disclosure relates to methods for generating spatially barcoded arrays using concentration gradients.
    Type: Application
    Filed: August 27, 2019
    Publication date: October 21, 2021
    Inventors: Eswar Prasad Ramachandran Iyer, Michael Schnall-Levin, Augusto Manuel Tentori, Tarjei Sigurd Mikkelsen, Benjamin Hindson, Michael Ybarra Lucero, Rajiv Bharadwaj, Yifeng Yin, Zachary Bent, Jennifer Chew, Meghan L. F. Frey, Linda Kvastad, Joakim Lundeberg, Eva Gracia Villacampa
  • Publication number: 20210292748
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: April 22, 2021
    Publication date: September 23, 2021
    Applicants: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Publication number: 20210292822
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: April 22, 2021
    Publication date: September 23, 2021
    Applicants: Spatial Transcriptomics AB, Illumina, Inc.
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Publication number: 20200399687
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: September 3, 2020
    Publication date: December 24, 2020
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 10774374
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Grant
    Filed: April 4, 2016
    Date of Patent: September 15, 2020
    Assignee: Spatial Transcriptomics AB and Illumina, Inc.
    Inventors: Jonas Frisén, Patrik Ståhl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Publication number: 20190264268
    Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.
    Type: Application
    Filed: January 22, 2019
    Publication date: August 29, 2019
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg
  • Publication number: 20190203275
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Application
    Filed: April 4, 2016
    Publication date: July 4, 2019
    Inventors: JONAS FRISÉN, PATRIK STÅHL, JOAKIM LUNDEBERG, GORDON M. CANN, LEILA BAZARGAN, ALEX ARAVANIS