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).
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Patent number: 12247249Abstract: 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: GrantFiled: December 17, 2019Date of Patent: March 11, 2025Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing
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Publication number: 20250051841Abstract: 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: ApplicationFiled: August 30, 2024Publication date: February 13, 2025Inventors: Samuel Woodhouse, Tim Forshew, Stefanie Lensing
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Patent number: 12084724Abstract: 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: GrantFiled: October 5, 2021Date of Patent: September 10, 2024Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20230304084Abstract: 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: ApplicationFiled: February 26, 2020Publication date: September 28, 2023Inventors: Samuel Woodhouse, Warren Emmett, Tim Forshew, Vincent Plagnol, Stefanie Lensing, Matthew Edward Smith, Giovanni Marsico, Mikidache Madi
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Publication number: 20220348998Abstract: 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: ApplicationFiled: May 31, 2022Publication date: November 3, 2022Inventors: Samuel Woodhouse, Tim Forshew, Stefanie Lensing
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Publication number: 20220162707Abstract: 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: ApplicationFiled: October 5, 2021Publication date: May 26, 2022Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20220056508Abstract: 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: ApplicationFiled: December 17, 2019Publication date: February 24, 2022Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing
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Patent number: 11168371Abstract: 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: GrantFiled: April 19, 2019Date of Patent: November 9, 2021Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20210139996Abstract: 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: ApplicationFiled: November 20, 2020Publication date: May 13, 2021Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Patent number: 10876170Abstract: 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: GrantFiled: June 18, 2018Date of Patent: December 29, 2020Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Patent number: 10533214Abstract: 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: GrantFiled: December 21, 2018Date of Patent: January 14, 2020Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing
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Publication number: 20200010905Abstract: 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: ApplicationFiled: June 18, 2018Publication date: January 9, 2020Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20190241975Abstract: 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: ApplicationFiled: April 19, 2019Publication date: August 8, 2019Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20190241976Abstract: 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: ApplicationFiled: April 19, 2019Publication date: August 8, 2019Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20190241977Abstract: 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: ApplicationFiled: April 19, 2019Publication date: August 8, 2019Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20190241978Abstract: 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: ApplicationFiled: April 19, 2019Publication date: August 8, 2019Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20190241974Abstract: 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: ApplicationFiled: April 19, 2019Publication date: August 8, 2019Inventors: Samuel Woodhouse, Stefanie Lensing, Tim Forshew, Vincent Plagnol, Matthew Edward Smith, Karen Howarth, Michael Epstein
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Publication number: 20190112645Abstract: 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: ApplicationFiled: December 21, 2018Publication date: April 18, 2019Inventors: Samuel Woodhouse, Giovanni Marsico, Vincent Plagnol, Stefanie Lensing