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: 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
  • Publication number: 20190024153
    Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array includes 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: July 23, 2018
    Publication date: January 24, 2019
    Inventors: JONAS FRISEN, PATRIK STÅHL, JOAKIM LUNDEBERG
  • Publication number: 20190024154
    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: July 23, 2018
    Publication date: January 24, 2019
    Inventors: JONAS FRISEN, PATRIK STÅHL, JOAKIM LUNDEBERG
  • Publication number: 20190017106
    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: June 20, 2018
    Publication date: January 17, 2019
    Inventors: JONAS FRISEN, PATRIK STÅHL, JOAKIM LUNDEBERG
  • Patent number: 10030261
    Abstract: The present invention relates to methods and products for the localized or spatial detection of nucleic acid in a tissue sample and in particular to a method for localized detection of nucleic acid in a tissue sample comprising: (a) providing an array comprising a substrate on which multiple species of capture probes are directly or indirectly immobilized such that each species occupies a distinct position on the array and is oriented to have a free 3? end to enable said probe to function as a primer for a primer extension or ligation reaction, wherein each species of said capture probe comprises a nucleic acid molecule with 5? to 3?: (i) a positional domain that corresponds to the position of the capture probe on the array, and (ii) a capture domain; (b) contacting said array with a tissue sample such that the position of a capture probe on the array may be correlated with a position in the tissue sample and allowing nucleic acid of the tissue sample to hybridize to the capture domain in said capture probes;
    Type: Grant
    Filed: April 13, 2012
    Date of Patent: July 24, 2018
    Assignee: SPATIAL TRANSCRIPTOMICS AB
    Inventors: Jonas Frisen, Patrik Ståhl, Joakim Lundeberg
  • Patent number: 9593365
    Abstract: The present invention relates to methods and products for localized or spatial detection and/or analysis of RNA in a tissue sample or a portion thereof, comprising: (a) providing an object substrate on which at least one species of capture probe, comprising a capture domain, is directly or indirectly immobilized such that the probes are oriented to have a free 3? end to enable said probe to function as a reverse transcriptase (RT) primer; (b) contacting said substrate with a tissue sample and allowing RNA of the tissue sample to hybridize to the capture probes; (c) generating cDNA molecules from the captured RNA molecules using said capture probes as RT primers; (d) labelling the cDNA molecules generated in step (c), wherein said labelling step may be contemporaneous with, or subsequent to, said generating step; (e) detecting a signal from the labelled cDNA molecules; and optionally (f) imaging the tissue sample, wherein the tissue sample is imaged before or after step (c).
    Type: Grant
    Filed: October 16, 2013
    Date of Patent: March 14, 2017
    Assignee: SPATIAL TRANSCRIPTIONS AB
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Fredrik Salmen
  • Publication number: 20150344942
    Abstract: The present invention relates to methods and products for localized or spatial detection and/or analysis of RNA in a tissue sample or a portion thereof, comprising: (a) providing an object substrate on which at least one species of capture probe, comprising a capture domain, is directly or indirectly immobilized such that the probes are oriented to have a free 3? end to enable said probe to function as a reverse transcriptase (RT) primer; (b) contacting said substrate with a tissue sample and allowing RNA of the tissue sample to hybridise to the capture probes; (c) generating cDNA molecules from the captured RNA molecules using said capture probes as RT primers; (d) labelling the cDNA molecules generated in step (c), wherein said labelling step may be contemporaneous with, or subsequent to, said generating step; (e) detecting a signal from the labelled cDNA molecules; and optionally (f) imaging the tissue sample, wherein the tissue sample is imaged before or after step (c).
    Type: Application
    Filed: October 16, 2013
    Publication date: December 3, 2015
    Inventors: JONAS FRISEN, PATRIK STAHL, JOAKIM LUNDEBERG, FREDRIK SALMEN
  • Publication number: 20140066318
    Abstract: The present invention relates to methods and products for the localized or spatial detection of nucleic acid in a tissue sample and in particular to a method for localized detection of nucleic acid in a tissue sample comprising: (a) providing an array comprising a substrate on which multiple species of capture probes are directly or indirectly immobilized such that each species occupies a distinct position on the array and is oriented to have a free 3? end to enable said probe to function as a primer for a primer extension or ligation reaction, wherein each species of said capture probe comprises a nucleic acid molecule with 5? to 3?: (i) a positional domain that corresponds to the position of the capture probe on the array, and (ii) a capture domain; (b) contacting said array with a tissue sample such that the position of a capture probe on the array may be correlated with a position in the tissue sample and allowing nucleic acid of the tissue sample to hybridize to the capture domain in said capture probes;
    Type: Application
    Filed: March 13, 2012
    Publication date: March 6, 2014
    Applicant: SPATIAL TRANSCRIPTOMICS AB
    Inventors: Jonas Frisen, Patrik Ståhl, Joakim Lundeberg
  • Patent number: 7262032
    Abstract: The present invention relates to a method of detecting a base at a pre-determined position in a nucleic acid molecule by performing enzymatic detection reactions using base-specific detection oligomers, where each oligomer is specific for a particular base at the predetermined position, and then comparing the enzymatic detection reactions to determine which base is present at the position, with an enzyme-disabling agent being present during the enzymatic detection reaction. In preferred embodiments the enzymatic detection reaction is an oligomer elongation extension reaction, catalysed by, among others, polymerase or ligase. Also disclosed are methods of performing the assay in a liquid phase and on microarrays.
    Type: Grant
    Filed: October 21, 2005
    Date of Patent: August 28, 2007
    Inventors: Afshin Ahmadian, Joakim Lundeberg
  • Publication number: 20060088872
    Abstract: The present invention relates to a method of detecting a base at a pre-determined position in a nucleic acid molecule by performing enzymatic detection reactions using base-specific detection oligomers, where each oligomer is specific for a particular base at the predetermined position, and then comparing the enzymatic detection reactions to determine which base is present at the position, with an enzyme-disabling agent being present during the enzymatic detection reaction. In preferred embodiments the enzymatic detection reaction is an oligomer elongation extension reaction, catalysed by, among others, polymerase or ligase. Also disclosed are methods of performing the assay in a liquid phase and on microarrays.
    Type: Application
    Filed: October 21, 2005
    Publication date: April 27, 2006
    Inventors: Afshin Ahmadian, Joakim Lundeberg
  • Patent number: 6610479
    Abstract: Enzymes or catalytic fragments thereof reversibly inactivated by attachment to an immobilizing moiety which may comprise a magnetic particle are activated by release from the immobilizing moiety. The enzyme or fragment may be in the form of a fusion protein that is attached to the immobilizing moiety via a pair of affinity binding partners such that the enzyme or fragment is reversibly inactivated, and release of the fusion protein from the immobilizing moiety activates the enzyme or fragment. Enzymes include DNA polymerases, DNA ligases, Reverse transcriptases and RNA polymerases. The enzyme or fragment may be thermostable, and the fusion protein can be bound to the immobilizing moiety via a heat-labile linkage. Activation of the reversibly inactivated immobilized enzyme or fragment has particular utility in PCR and analogous nucleic acid amplification techniques.
    Type: Grant
    Filed: February 13, 1998
    Date of Patent: August 26, 2003
    Assignee: Dynal AS
    Inventors: Joakim Lundeberg, Mathias Uhlén
  • Publication number: 20030157499
    Abstract: The present invention provides a method of assessing the amount of target nucleic acid in a sample which comprises co-amplifying the target nucleic acid and at least one competitor nucleic acid molecule wherein each competitor molecule contains a unique discriminatory sequence, and determining the relative amounts of the respective amplicons, characterised in that determination is achieved by detecting a primer extension reaction using each said amplicon as template and a kit for use in such a method.
    Type: Application
    Filed: October 29, 2002
    Publication date: August 21, 2003
    Inventors: Joakim Lundeberg, Mostafa Ronaghi
  • Publication number: 20030104372
    Abstract: The present invention provides methods of allele-specific primer extension useful for detecting mutations and genetic variations.
    Type: Application
    Filed: February 23, 2001
    Publication date: June 5, 2003
    Applicant: PYROSEQUENCING AB.
    Inventors: Afshin Ahmadian, Joakim Lundeberg, Pal Nyren
  • Patent number: 6482592
    Abstract: The invention provides a method of improving the binding of a series of consecutive nucleotide bases to a complementary target nucleic acid molecule in a sample, wherein said method comprises at least the step or steps of binding a complementary modular oligonucleotide of at least two parts (modules) including said nucleotide bases to adjacent stretches of said target nucleic acid molecule in said sample, especially methods of detection/isolation, particularly in the isolation of primer extension products and methods in which the modular oligonucleotide is a primer, modular oligonucleotides themselves and their use in methods of the invention.
    Type: Grant
    Filed: September 15, 1998
    Date of Patent: November 19, 2002
    Assignee: Dynal AS
    Inventors: Joakim Lundeberg, Mathias Uhlen
  • Patent number: 5534424
    Abstract: The invention provides a method of identification of the base in a target position in a DNA sequence wherein sample DNA is subjected to amplification; the amplified DNA is immobilised and then subjected to strand separation, the non-immobilised strand being removed and an extension primer, which hybridises to the immobilised DNA immediately adjacent to the target position, is provided; each of four aliquots of the immobilised single stranded DNA is then subjected to a polymerase reaction in the presence of a dideoxynucleotide, each aliquot using a different dideoxynucleotide whereby only the dideoxynucleotide whereby only the dideoxynucleotide complementary to the base in the target position becomes incorpored; the four aliquots are then subjected to extension in the presence of all four deoxynucleotides, whereby in each aliquot the DNA which has not reacted with the dideoxynucleotide is extended to form double stranded DNA while the dideoxy-blocked DNA remains as non-extended DNA; followed by identification
    Type: Grant
    Filed: April 18, 1995
    Date of Patent: July 9, 1996
    Assignee: Cemu Bioteknik AB
    Inventors: Mathias Uhlen, Joakim Lundeberg