Patents by Inventor Stefanie Lensing

Stefanie Lensing 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).

  • Patent number: 12247249
    Abstract: Provided herein is method for, among other things, estimating the number of sequence variations in a sample of DNA. In some embodiments, the method can be used to estimate the mutational load of a sample. In some embodiments, the method makes use of a set of primers that have 3? ends that specifically hybridizes to a sequence that is repeated multiple times in the genome. Thermocycling a reaction mix containing the primers may produce a reaction product comprising at least 50 amplicons having a total length of at least 100 kb. This product can be sequenced to provide an estimate of the number of sequence variations in the sample, and thus the mutational load of the sample.
    Type: Grant
    Filed: December 17, 2019
    Date of Patent: March 11, 2025
    Assignee: INIVATA LTD.
    Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing
  • Publication number: 20250051841
    Abstract: A method of sequencing a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise providing a sample from a patient, the sample having cell-free DNA molecules comprising NAOIs, amplifying the NAOIs, ligating adapters to the NAOIs, and sequencing the NAOIs. A method of labelling a NAOIs is also provided. In some embodiments, the method may comprise providing a sample from a patient having the NAOIs, amplifying the NAOIs, contacting the amplified NAOIs with a pool of oligonucleotides, attaching oligonucleotides to each of the amplified NAOIs to label the NAOIs. The method may further comprise sequencing the labelled NAOIs and grouping the resulting sequencing reads.
    Type: Application
    Filed: August 30, 2024
    Publication date: February 13, 2025
    Inventors: Samuel Woodhouse, Tim Forshew, Stefanie Lensing
  • Patent number: 12084724
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Grant
    Filed: October 5, 2021
    Date of Patent: September 10, 2024
    Assignee: INIVATA LTD.
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20230304084
    Abstract: Provided herein is method for quantifying a target sequence in a sample. In some embodiments, the method may comprise: adding a known amount of a first nucleic acid to a sample, wherein the longest contiguous sequence that the first spike-in sequence and the first target sequence have in common is no more than 40 contiguous nucleotides. After amplification and sequencing the reads from first nucleic acid can be used to quantify the amount of target sequence, or a variant thereof in the sample.
    Type: Application
    Filed: February 26, 2020
    Publication date: September 28, 2023
    Inventors: Samuel Woodhouse, Warren Emmett, Tim Forshew, Vincent Plagnol, Stefanie Lensing, Matthew Edward Smith, Giovanni Marsico, Mikidache Madi
  • Publication number: 20220348998
    Abstract: The invention relates to methods for labelling individual nucleic acid molecules present in a sample, comprising contacting the nucleic acid molecules with an adaptor or mixture of adaptors, wherein the adaptor or adaptors comprise one or more universal nucleotide bases and a ligation moiety at their 3? end, and ligating an adaptor to the nucleic acid of interest, wherein the adaptor is ligated to the nucleic acid molecules at the 3? end of the adaptor. A random tag is then generated in situ by conducting an extension reaction over the ligated adaptor. Methods of the invention may be used to detect genetic alterations or variants in any nucleic acid with high specificity and high sensitivity, including mutations in nucleic acids such as ctDNA, cfDNA, and in viral, microbiome and plant nucleic acids. Methods of the invention may also be used in detection and correction of errors introduced into nucleic acids during processing.
    Type: Application
    Filed: May 31, 2022
    Publication date: November 3, 2022
    Inventors: Samuel Woodhouse, Tim Forshew, Stefanie Lensing
  • Publication number: 20220162707
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: October 5, 2021
    Publication date: May 26, 2022
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20220056508
    Abstract: Provided herein is method for, among other things, estimating the number of sequence variations in a sample of DNA. In some embodiments, the method can be used to estimate the mutational load of a sample. In some embodiments, the method makes use of a set of primers that have 3? ends that specifically hybridizes to a sequence that is repeated multiple times in the genome. Thermocycling a reaction mix containing the primers may produce a reaction product comprising at least 50 amplicons having a total length of at least 100 kb. This product can be sequenced to provide an estimate of the number of sequence variations in the sample, and thus the mutational load of the sample.
    Type: Application
    Filed: December 17, 2019
    Publication date: February 24, 2022
    Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing
  • Patent number: 11168371
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Grant
    Filed: April 19, 2019
    Date of Patent: November 9, 2021
    Assignee: INIVATA LTD.
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20210139996
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: November 20, 2020
    Publication date: May 13, 2021
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Patent number: 10876170
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Grant
    Filed: June 18, 2018
    Date of Patent: December 29, 2020
    Assignee: INIVATA LTD.
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Patent number: 10533214
    Abstract: Provided herein is method for, among other things, estimating the number of sequence variations in a sample of DNA. In some embodiments, the method can be used to estimate the mutational load of a sample. In some embodiments, the method makes use of a set of primers that have 3? ends that specifically hybridizes to a sequence that is repeated multiple times in the genome. Thermocycling a reaction mix containing the primers may produce a reaction product comprising at least 50 amplicons having a total length of at least 100 kb. This product can be sequenced to provide an estimate of the number of sequence variations in the sample, and thus the mutational load of the sample.
    Type: Grant
    Filed: December 21, 2018
    Date of Patent: January 14, 2020
    Assignee: INIVATA LTD.
    Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing
  • Publication number: 20200010905
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: June 18, 2018
    Publication date: January 9, 2020
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20190241975
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: April 19, 2019
    Publication date: August 8, 2019
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20190241976
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: April 19, 2019
    Publication date: August 8, 2019
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20190241977
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: April 19, 2019
    Publication date: August 8, 2019
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20190241978
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: April 19, 2019
    Publication date: August 8, 2019
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20190241974
    Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.
    Type: Application
    Filed: April 19, 2019
    Publication date: August 8, 2019
    Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
  • Publication number: 20190112645
    Abstract: Provided herein is method for, among other things, estimating the number of sequence variations in a sample of DNA. In some embodiments, the method can be used to estimate the mutational load of a sample. In some embodiments, the method makes use of a set of primers that have 3? ends that specifically hybridizes to a sequence that is repeated multiple times in the genome. Thermocycling a reaction mix containing the primers may produce a reaction product comprising at least 50 amplicons having a total length of at least 100 kb. This product can be sequenced to provide an estimate of the number of sequence variations in the sample, and thus the mutational load of the sample.
    Type: Application
    Filed: December 21, 2018
    Publication date: April 18, 2019
    Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing