Patents Assigned to Cambridge Epigenetix Limited
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Patent number: 11608518Abstract: Provided herein are methods, systems, and compositions for determining a base in a polynucleotide. In various aspects, the methods, systems, and compositions presented herein are useful for performing 4-base, 5-base, or 6-base sequencing of polynucleotide molecules, for example, from liquid biopsy samples or wherein the base is a low frequency mutation.Type: GrantFiled: March 21, 2022Date of Patent: March 21, 2023Assignee: Cambridge Epigenetix LimitedInventors: Shankar Balasubramanian, Jens Fullgrabe, Walraj Singh Gosal, Joanna Dawn Holbrook, Sidong Liu, David Morley, Oliver Nentwich, Tobias Ost, Michael Steward, Albert Vilella, Nicolas James Walker, Shirong Yu, Helen Rachel Bignell, Rita Santo San-Bento
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Patent number: 10563248Abstract: This invention relates to the use of metal (VI) oxo complexes to catalyse the selective oxidation of 5hmC residues in polynucleotides to 5fC residues. This may be useful in the identification of modified cytosine residues in a population of polynucleotides comprising a sample nucleotide sequence. A first portion of the population is oxidised with a metal (VI) oxo complex and then the first portion and a second portion of said population are both treated with bisulfite. The residues in the first and second portions that correspond to a cytosine residue in the sample nucleotide sequence are identified following treatment and the identities of these residues are used to determine the modification of the cytosine residue in the sample nucleotide sequence. Methods, reagents and kits are provided.Type: GrantFiled: November 28, 2013Date of Patent: February 18, 2020Assignee: Cambridge Epigenetix LimitedInventor: Toby Ost
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Patent number: 10428381Abstract: This invention relates to the identification of modified cytosine residues, such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) to be distinguished from cytosine (C) in a sample nucleotide sequence. Methods may comprise oxidizing or reducing a first portion of polynucleotides which comprise the sample nucleotide sequence; treating the oxidized or reduced first portion and a second portion of polynucleotides with bisulfite; sequencing the polynucleotides in the first and second portions of the population following steps ii) and iii) to produce first and second nucleotide sequences, respectively and; identifying the residue in the first and second nucleotide sequences which corresponds to a cytosine residue in the sample nucleotide sequence. These methods may be useful, for example in the analysis of genomic DNA and/or of RNA.Type: GrantFiled: March 21, 2016Date of Patent: October 1, 2019Assignee: Cambridge Epigenetix LimitedInventors: Michael John Booth, Shankar Balasubramanian
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Patent number: 9822394Abstract: This invention relates to the preparation of nucleic acid samples for analysis. The invention may be particularly useful for single stranded samples. Embodiments of the invention involve the attachment of double stranded or hairpin oligonucleotides using template independent polymerase enzymes in the preparation of nucleic acid sequencing libraries.Type: GrantFiled: February 26, 2016Date of Patent: November 21, 2017Assignee: CAMBRIDGE EPIGENETIX LIMITEDInventors: Tobias William Barr Ost, Neil Matthew Bell
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Patent number: 9290807Abstract: This invention relates to the identification of modified cytosine residues, such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) to be distinguished from cytosine (C) in a sample nucleotide sequence. Methods may comprise oxidizing or reducing a first portion of polynucleotides which comprise the sample nucleotide sequence; treating the oxidized or reduced first portion and a second portion of polynucleotides with bisulfite; sequencing the polynucleotides in the first and second portions of the population following steps ii) and iii) to produce first and second nucleotide sequences, respectively and; identifying the residue in the first and second nucleotide sequences which corresponds to a cytosine residue in the sample nucleotide sequence. These methods may be useful, for example in the analysis of genomic DNA and/or of RNA.Type: GrantFiled: July 27, 2012Date of Patent: March 22, 2016Assignee: Cambridge Epigenetix LimitedInventors: Michael John Booth, Shankar Balasubramanian
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Publication number: 20150299781Abstract: This invention relates to the use of metal (VI) oxo complexes to catalyse the selective oxidation of 5hmC residues in polynucleotides to 5fC residues. This may be useful in the identification of modified cytosine residues in a population of polynucleotides comprising a sample nucleotide sequence. A first portion of the population is oxidised with a metal (VI) oxo complex and then the first portion and a second portion of said population are both treated with bisulfite. The residues in the first and second portions that correspond to a cytosine residue in the sample nucleotide sequence are identified following treatment and the identities of these residues are used to determine the modification of the cytosine residue in the sample nucleotide sequence. Methods, reagents and kits are provided.Type: ApplicationFiled: November 28, 2013Publication date: October 22, 2015Applicant: Cambridge Epigenetix LimitedInventor: Toby Ost
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Publication number: 20140178881Abstract: This invention relates to the identification of modified cytosine residues, such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) to be distinguished from cytosine (C) in a sample nucleotide sequence. Methods may comprise oxidising or reducing a first portion of polynucleotides which comprise the sample nucleotide sequence; treating the oxidised or reduced first portion and a second portion of polynucleotides with bisulfite; sequencing the polynucleotides in the first and second portions of the population following steps ii) and iii) to produce first and second nucleotide sequences, respectively and; identifying the residue in the first and second nucleotide sequences which corresponds to a cytosine residue in the sample nucleotide sequence. These methods may be useful, for example in the analysis of genomic DNA and/or of RNA.Type: ApplicationFiled: July 27, 2012Publication date: June 26, 2014Applicant: Cambridge Epigenetix LimitedInventors: Michael John Booth, Shankar Balasubramanian