Patents by Inventor Vincent Plagnol
Vincent Plagnol 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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Publication number: 20240110224Abstract: Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).Type: ApplicationFiled: September 13, 2023Publication date: April 4, 2024Inventors: Vincent Plagnol, Tim Forshew, Samuel Woodhouse, Andrew Lawson, Matthew Smith
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Patent number: 11788116Abstract: A method for the analysis of minimal residual disease is provided. In some embodiments, the method comprises obtaining multiple pairs of primers designed to amplify sequences that contain a plurality of sequence variations that have been previously identified in a patient's tumor. Amplicons are then obtained through a targeted multiplex amplification that amplifies those sequences from cell-free DNA isolated from a plasma sample. The amplicons are sequenced and two or more of the sequence variations are detected from sequence reads, wherein the detecting comprises comparing a quantity of sequence reads containing a sequence variation against a threshold value. A score is then calculated for the patient sample based on the combined allele frequencies of the detected two or more sequence variations, wherein the score indicates the presence of minimal residual disease.Type: GrantFiled: March 17, 2023Date of Patent: October 17, 2023Assignee: INIVATA LTD.Inventors: Vincent Plagnol, Tim Forshew, Samuel Woodhouse, Andrew Lawson, Matthew Smith
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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: 20230227890Abstract: Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).Type: ApplicationFiled: March 17, 2023Publication date: July 20, 2023Inventors: Vincent Plagnol, Tim Forshew, Samuel Woodhouse, Andrew Lawson, Matthew Smith
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Patent number: 11566274Abstract: Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).Type: GrantFiled: January 22, 2020Date of Patent: January 31, 2023Assignee: INIVATA LTD.Inventors: Vincent Plagnol, Tim Forshew, Samuel Woodhouse, Andrew Lawson, Matthew Smith
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Publication number: 20220364186Abstract: Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and/or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.Type: ApplicationFiled: June 2, 2022Publication date: November 17, 2022Inventors: Clive Morris, Vincent Plagnol, Tim Forshew
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Patent number: 11377698Abstract: Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and/or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.Type: GrantFiled: September 4, 2019Date of Patent: July 5, 2022Assignee: INIVATA LTD.Inventors: Clive Morris, Vincent Plagnol, Tim Forshew
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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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Publication number: 20220017970Abstract: The present disclosure provides, among other things, a way to quantify gene fusions in cell-free DNA. The method may be used to determine if the abundance of the fusion molecules has changed over time.Type: ApplicationFiled: December 11, 2019Publication date: January 20, 2022Inventors: Karen Howarth, Samuel Woodhouse, Tim Forshew, Vincent Plagnol
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Patent number: 11186878Abstract: A method for analyzing cell free DNA (cfDNA) from the bloodstream of a cancer patient is provided. In some embodiments, the method may comprise sequencing at least part of the coding sequences of TP53 and KRAS in a sample of the cfDNA, analyzing the sequences to identify nucleotide transversions in the coding sequences of the genes, relative to reference sequences of the genes. In some embodiments, the method may comprise counting the total number of identified nucleotide transversions. The presence of nucleotide transversions indicates that the patient will be more responsive to the immune checkpoint inhibitor, whereas a decreased number of transversions or no transversios indicates that the patient will be less responsive to the immune checkpoint inhibitor.Type: GrantFiled: May 23, 2019Date of Patent: November 30, 2021Assignee: INIVATA LTD.Inventors: John Beeler, Vincent Plagnol, Greg Jones
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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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Publication number: 20210040564Abstract: A method for analyzing cell free DNA (cfDNA) from the bloodstream of a cancer patient is provided. In some embodiments, the method may comprise sequencing at least part of the coding sequences of TP53 and KRAS in a sample of the cfDNA, analyzing the sequences to identify nucleotide transversions in the coding sequences of the genes, relative to reference sequences of the genes. In some embodiments, the method may comprise counting the total number of identified nucleotide transversions. The presence of nucleotide transversions indicates that the patient will be more responsive to the immune checkpoint inhibitor, whereas a decreased number of transversions or no transversios indicates that the patient will be less responsive to the immune checkpoint inhibitor.Type: ApplicationFiled: April 19, 2019Publication date: February 11, 2021Inventors: John Beeler, Vincent Plagnol, Greg Jones, Giovanni Marsico
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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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Publication number: 20200157604Abstract: Provided herein is a method for sequence analysis that comprises analyzing PCR reactions that each contain different portions of the same sample, wherein at least some of the primer pairs are in more than one PCR reaction and at least one of the PCR reactions contains some but not all of the primer pairs of the other reaction(s).Type: ApplicationFiled: January 22, 2020Publication date: May 21, 2020Inventors: Vincent Plagnol, Tim Forshew, Samuel Woodhouse, Andrew Lawson, Matthew Smith
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Publication number: 20200071772Abstract: Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and/or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.Type: ApplicationFiled: September 4, 2019Publication date: March 5, 2020Inventors: Clive Morris, Vincent Plagnol, Tim Forshew
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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: 20190352723Abstract: A method for analyzing cell free DNA (cfDNA) from the bloodstream of a cancer patient is provided. In some embodiments, the method may comprise sequencing at least part of the coding sequences of TP53 and KRAS in a sample of the cfDNA, analyzing the sequences to identify nucleotide transversions in the coding sequences of the genes, relative to reference sequences of the genes. In some embodiments, the method may comprise counting the total number of identified nucleotide transversions. The presence of nucleotide transversions indicates that the patient will be more responsive to the immune checkpoint inhibitor, whereas a decreased number of transversions or no transversios indicates that the patient will be less responsive to the immune checkpoint inhibitor.Type: ApplicationFiled: May 23, 2019Publication date: November 21, 2019Inventors: John Beeler, Vincent Plagnol, Greg Jones