Patents Assigned to Rubicon Genomics, Inc.
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Publication number: 20170314069Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: ApplicationFiled: February 13, 2017Publication date: November 2, 2017Applicant: Rubicon Genomics, Inc.Inventors: Vladimir L. MAKAROV, Emmanuel KAMBEROV, Brendan J. TARRIER
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Patent number: 9708652Abstract: The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries.Type: GrantFiled: April 9, 2013Date of Patent: July 18, 2017Assignee: RUBICON GENOMICS, INC.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Tong Sun, Jonathan H. Pinter, Brendan J. Tarrier, Eric E. Bruening, Takao Kurihara, Tim Tesmer, Joseph M'Mwirichia
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Patent number: 9598727Abstract: The present invention is directed generally to the use of stem-loop oligonucleotides comprising an inverted repeat, a loop, and at least one degradable site or site capable of becoming a degradable site in the preparation of DNA molecules, such as a library. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: GrantFiled: April 11, 2014Date of Patent: March 21, 2017Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
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Publication number: 20170037460Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: ApplicationFiled: August 5, 2016Publication date: February 9, 2017Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. MAKAROV, Irina SLEPTSOVA, Emmanuel KAMBEROV, Eric BRUENING
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Publication number: 20160355879Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: ApplicationFiled: July 22, 2016Publication date: December 8, 2016Applicant: Rubicon Genomics, Inc.Inventors: Emmanuel KAMBEROV, Tong SUN, Eric BRUENING, Jonathon H. PINTER, Irina SLEPTSOVA, Takao KURIHARA, Vladimir L. MAKAROV
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Publication number: 20160289723Abstract: Provided herein are compositions for and methods of generating ligation-competent nucleic acids. In some aspects, the compositions comprise Exonuclease III, T4 DNA Polymerase, Klenow, and/or T4 polynucleotide kinase.Type: ApplicationFiled: March 30, 2016Publication date: October 6, 2016Applicant: Rubicon Genomics, Inc.Inventors: Emmanuel KAMBEROV, John LANGMORE, Tim TESMER, Marta GONZALEZ-PLASKY
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Publication number: 20160257985Abstract: The present disclosure provides systems, processes, articles of manufacture, and compositions that relate to the use of degradable adaptors for background reduction in various nucleic acid manipulations. In particular, adaptors are provided that can be degraded to an extent that the degradation products are incapable or are substantially incapable from participating in subsequent reactions, such as ligation, primer extension, amplification, and sequencing reactions.Type: ApplicationFiled: November 18, 2014Publication date: September 8, 2016Applicant: RUBICON GENOMICS, INC.Inventors: Emmanuel Kamberov, John Langmore, Tim Tesmer
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Patent number: 9410193Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: GrantFiled: August 4, 2014Date of Patent: August 9, 2016Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
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Publication number: 20150284712Abstract: Methods of barcoding nucleic acids, such as genomic DNA, are provided herein. In some embodiments, a fragment of genomic DNA may comprise a first and a second barcode.Type: ApplicationFiled: November 5, 2013Publication date: October 8, 2015Applicant: Rubicon Genomics, Inc.Inventors: Takao Kurihara, Emmanuel Kamberov, Tim Tesmer, John Langmore
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Publication number: 20150087528Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: ApplicationFiled: August 4, 2014Publication date: March 26, 2015Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. MAKAROV, Irina SLEPTSOVA, Emmanuel KAMBEROV, Eric BRUENING
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Publication number: 20150079637Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: ApplicationFiled: April 11, 2014Publication date: March 19, 2015Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. MAKAROV, Emmanuel KAMBEROV, Brendan J. TARRIER
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Patent number: 8815504Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: GrantFiled: February 1, 2010Date of Patent: August 26, 2014Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
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Patent number: 8778610Abstract: The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.Type: GrantFiled: February 27, 2013Date of Patent: July 15, 2014Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
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Patent number: 8728737Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: GrantFiled: February 13, 2013Date of Patent: May 20, 2014Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
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Publication number: 20130316913Abstract: The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.Type: ApplicationFiled: February 27, 2013Publication date: November 28, 2013Applicant: Rubicon Genomics, Inc.Inventor: Rubicon Genomics, Inc.
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Publication number: 20130309668Abstract: The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries.Type: ApplicationFiled: April 9, 2013Publication date: November 21, 2013Applicant: Rubicon Genomics, Inc.Inventor: Rubicon Genomics, Inc.
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Patent number: 8409804Abstract: The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.Type: GrantFiled: March 2, 2006Date of Patent: April 2, 2013Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier
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Patent number: 8206913Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: March 3, 2010Date of Patent: June 26, 2012Assignee: Rubicon Genomics, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Publication number: 20120142060Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: ApplicationFiled: November 1, 2011Publication date: June 7, 2012Applicant: Rubicon Genomics, Inc.Inventors: VLADIMIR L. MAKAROV, Emmanuel Kamberov, Brendan J. Tarrier
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Patent number: 8071312Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.Type: GrantFiled: September 28, 2010Date of Patent: December 6, 2011Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Emmanuel Kamberov, Brendan J. Tarrier