Patents Assigned to Population Genetics Technologies Ltd
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Patent number: 9920355Abstract: Providing herein, among other things, is a method for preparing a nucleic acid for sequencing. In some embodiments, the method comprises a) amplifying a nucleic acid template using a dNTP mix that contains 5-methyl dCTP, thereby producing product nucleic acid molecules that contains methylcytosines; b) digesting the product nucleic acid molecules with a methylation-dependent restriction endonuclease, thereby cleaving the product nucleic acid molecules at sites that are adjacent to at least some of the methylcytosine and producing fragments of the product nucleic acid molecules; and c) ligating double-stranded adaptors onto the ends of the fragments to produce adaptor-ligated products.Type: GrantFiled: November 12, 2015Date of Patent: March 20, 2018Assignee: POPULATION GENETICS TECHNOLOGIES LTD.Inventors: Robert Osborne, Samuel Woodhouse, Esther Musgrave-Brown
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Patent number: 9670536Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: GrantFiled: May 8, 2014Date of Patent: June 6, 2017Assignee: POPULATION GENETICS TECHNOLOGIES LTD.Inventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Patent number: 9670529Abstract: Described herein is a method for adding a counter sequence to the individual polynucleotide molecules of an initial nucleic acid sample. After addition of the counter sequence, the sample may be amplified and the number of initial target molecules in the sample can be estimated by counting the number of counter sequences associated with the amplified target molecules.Type: GrantFiled: February 26, 2013Date of Patent: June 6, 2017Assignee: POPULATION GENETICS TECHNOLOGIES LTD.Inventors: Robert Osborne, James Casbon, Andreas Claas, Gi Mikawa, Esther Musgrave-Brown
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Patent number: 9194001Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.Type: GrantFiled: February 24, 2015Date of Patent: November 24, 2015Assignee: Population Genetics Technologies Ltd.Inventor: Sydney Brenner
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Patent number: 9102980Abstract: Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or multiplex indentifier). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.Type: GrantFiled: February 4, 2014Date of Patent: August 11, 2015Assignee: Population Genetics Technologies LTD.Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
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Patent number: 9096952Abstract: Aspects of the present invention are drawn to methods and compositions for the genetic analysis of regions of interest (ROI) from one or more starting polynucleotide sample(s). In certain aspects, adapter tagged polynucleotide fragments from a plurality of initial polynucleotide samples are pooled, circularized and amplified to produce an immortalized library. Multiple ROI's from this immortalized library are amplified (e.g., in independent iPCR reactions) to generate amplicons, and, in some embodiments, pooled to form a pooled ROI amplicon sample. In certain embodiments, the amplicons for each ROI amplicon in the pooled ROI amplicon sample are present at known molar or mass ratios. The pooled ROI amplicon sample can be analyzed/processed as desired, e.g., sequenced using next generation sequencing technology.Type: GrantFiled: June 20, 2011Date of Patent: August 4, 2015Assignee: Population Genetics Technologies LTD.Inventors: Robert Osborne, Andrew Slatter
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Publication number: 20150197786Abstract: Described herein is a method for adding a counter sequence to the individual polynucleotide molecules of an initial nucleic acid sample. After addition of the counter sequence, the sample may be amplified and the number of initial target molecules in the sample can be estimated by counting the number of counter sequences associated with the amplified target molecules.Type: ApplicationFiled: February 26, 2013Publication date: July 16, 2015Applicant: Population Genetics Technologies Ltd.Inventors: Robert Osborne, James Casbon, Andreas Claas, Gi Mikawa, Esther Musgrave-Brown
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Patent number: 9018365Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.Type: GrantFiled: March 28, 2013Date of Patent: April 28, 2015Assignee: Population Genetics Technologies LtdInventor: Sydney Brenner
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Publication number: 20150031559Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: ApplicationFiled: May 8, 2014Publication date: January 29, 2015Applicant: Population Genetics Technologies LtdInventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Publication number: 20140272985Abstract: Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.Type: ApplicationFiled: February 4, 2014Publication date: September 18, 2014Applicant: Population Genetics Technologies LTDInventors: SYDNEY BRENNER, GI MIKAWA, ROBERT OSBORNE, ANDREW SLATTER
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Patent number: 8741606Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: GrantFiled: March 29, 2013Date of Patent: June 3, 2014Assignee: Population Genetics Technologies Ltd.Inventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Patent number: 8728766Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: GrantFiled: March 29, 2013Date of Patent: May 20, 2014Assignee: Population Genetics Technologies Ltd.Inventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Patent number: 8722368Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: GrantFiled: March 29, 2013Date of Patent: May 13, 2014Assignee: Population Genetics Technologies Ltd.Inventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Patent number: 8715967Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: GrantFiled: March 29, 2013Date of Patent: May 6, 2014Assignee: Population Genetics Technologies Ltd.Inventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Patent number: 8685678Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: GrantFiled: March 28, 2013Date of Patent: April 1, 2014Assignee: Population Genetics Technologies LtdInventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas
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Patent number: 8679756Abstract: Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.Type: GrantFiled: September 9, 2013Date of Patent: March 25, 2014Assignee: Population Genetics Technologies LtdInventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
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Publication number: 20140073512Abstract: Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.Type: ApplicationFiled: September 9, 2013Publication date: March 13, 2014Applicant: Population Genetics Technologies LtdInventors: SYDNEY BRENNER, GI MIKAWA, ROBERT OSBORNE, ANDREW SLATTER
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Publication number: 20140011708Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.Type: ApplicationFiled: March 28, 2013Publication date: January 9, 2014Applicant: Population Genetics Technologies LtdInventor: Sydney Brenner
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Patent number: 8563274Abstract: Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.Type: GrantFiled: April 9, 2013Date of Patent: October 22, 2013Assignee: Population Genetics Technologies LtdInventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
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Publication number: 20130237458Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.Type: ApplicationFiled: March 29, 2013Publication date: September 12, 2013Applicant: Population Genetics Technologies LtdInventors: James Casbon, Sydney Brenner, Robert Osborne, Conrad Lichtenstein, Andreas Claas