Patents by Inventor Samuel Woodhouse
Samuel Woodhouse 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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Publication number: 20240026440Abstract: A method of labelling a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise contacting a sample comprising the nucleic acid of interest with a pool of oligonucleotides, the pool comprising oligonucleotides having at least 5 different lengths; and attaching an oligonucleotide from the pool on to one or each end of the nucleic acid of interest, wherein attachment of an oligonucleotide moves the read start and/or stop coordinate when the labelled NAOI is sequenced.Type: ApplicationFiled: May 5, 2023Publication date: January 25, 2024Inventors: Samuel WOODHOUSE, Tim FORSHEW, Stefanie Viola LENSING
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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: 20230280242Abstract: The present invention relates to an apparatus for the disaggregation of tissue. The apparatus comprises a first cutting zone comprising a first cutting blade configured to rotate about a first rotational axis, and an opening for the ingress of tissue. The opening is oriented at an angle to the first rotational axis.Type: ApplicationFiled: August 4, 2021Publication date: September 7, 2023Inventors: Toby Proctor, Riccardo Rayan Siena, Joanne Wei-Gnan Tang, Duncan Young, Simon Waddelow, Michelle Griffin, Samuel Woodhouse, John Briant, Matthew Parker
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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: 11674175Abstract: A method of labelling a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise contacting a sample comprising the nucleic acid of interest with a pool of oligonucleotides, the pool comprising oligonucleotides having at least 5 different lengths; and attaching an oligonucleotide from the pool on to one or each end of the nucleic acid of interest, wherein attachment of an oligonucleotide moves the read start and/or stop coordinate when the labelled NAOI is sequenced.Type: GrantFiled: March 7, 2019Date of Patent: June 13, 2023Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Tim Forshew, Stefanie Viola Lensing
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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: 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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Patent number: 11359233Abstract: 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: GrantFiled: September 13, 2017Date of Patent: June 14, 2022Assignee: INIVATA LTD.Inventors: Samuel Woodhouse, Tim Forshew, Stefanie Viola 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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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: 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: 20210024993Abstract: Described herein, among other things, is a method of sequencing nucleic acids of interest (NAOIs). In some embodiments the method may comprise: providing a sample comprising NAOIs; attaching oligonucleotides to the NAOIs to provide labelled NAOIs, wherein the oligonucleotides comprise a PCR cycle counter generator sequence comprising at least one universal nucleotide base; amplifying the labelled NAOIs using PCR to provide an amplified library of NAOIs each containing a PCR cycle counter sequence; sequencing the amplified library of NAOIs to provide a set of sequence reads, wherein each sequence read comprises a NAOI-originating component and a PCR cycle counter component; and distinguishing true variants in NAOI sequences from false variants in NAOI sequences.Type: ApplicationFiled: March 7, 2019Publication date: January 28, 2021Inventors: Samuel WOODHOUSE, Tim FORSHEW, Stefanie Viola LENSING
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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: 20200399694Abstract: A method of labelling a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise contacting a sample comprising the nucleic acid of interest with a pool of oligonucleotides, the pool comprising oligonucleotides having at least 5 different lengths; and attaching an oligonucleotide from the pool on to one or each end of the nucleic acid of interest, wherein attachment of an oligonucleotide moves the read start and/or stop coordinate when the labelled NAOI is sequenced.Type: ApplicationFiled: March 7, 2019Publication date: December 24, 2020Inventors: Samuel WOODHOUSE, Tim FORSHEW, Stefanie Viola LENSING
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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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Patent number: D1001266Type: GrantFiled: February 3, 2021Date of Patent: October 10, 2023Assignee: Achilles Therapeutics UK LimitedInventors: Toby Joseph Proctor, Riccardo Rayan Siena, Joanne Wei-Gnan Tang, Simon Waddelow, Michelle Griffin, Samuel Woodhouse, John Briant, Matthew Parker, Duncan Young