Patents Assigned to Callida Genomics, Inc.
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Patent number: 8445194Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: GrantFiled: June 13, 2006Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8440397Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: GrantFiled: October 31, 2007Date of Patent: May 14, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
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Patent number: 8133719Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: GrantFiled: October 31, 2007Date of Patent: March 13, 2012Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8105771Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: GrantFiled: February 26, 2004Date of Patent: January 31, 2012Assignee: Callida Genomics, Inc.Inventor: Radoje T. Drmanac
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Publication number: 20110319281Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.Type: ApplicationFiled: January 31, 2011Publication date: December 29, 2011Applicant: CALLIDA GENOMICS, INC.Inventor: Radoje DRMANAC
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Publication number: 20110281738Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: ApplicationFiled: May 2, 2011Publication date: November 17, 2011Applicant: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Patent number: 8034566Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: GrantFiled: October 30, 2007Date of Patent: October 11, 2011Assignee: Callida Genomics, Inc.Inventors: Radoje T. Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Patent number: 7960104Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: GrantFiled: September 29, 2006Date of Patent: June 14, 2011Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Publication number: 20110071053Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: September 15, 2010Publication date: March 24, 2011Applicant: Callida Genomics, Inc.Inventors: Radoje DRMANAC, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 7910304Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: GrantFiled: October 31, 2007Date of Patent: March 22, 2011Assignee: Callida Genomics, Inc.Inventor: Radoje T. Drmanac
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Patent number: 7906285Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: GrantFiled: October 31, 2007Date of Patent: March 15, 2011Assignee: Callida Genomics, Inc.Inventor: Radoje T. Drmanac
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Patent number: 7901891Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.Type: GrantFiled: December 15, 2008Date of Patent: March 8, 2011Assignee: Callida Genomics, Inc.Inventor: Radoje Drmanac
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Publication number: 20110039731Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and set of pools of probes, as well as method of generating pools of probes.Type: ApplicationFiled: December 22, 2009Publication date: February 17, 2011Applicant: CALLIDA GENOMICS, INC.Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Patent number: 7709197Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.Type: GrantFiled: June 13, 2006Date of Patent: May 4, 2010Assignee: Callida Genomics, Inc.Inventor: Radoje Drmanac
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Publication number: 20090311691Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.Type: ApplicationFiled: December 15, 2008Publication date: December 17, 2009Applicant: CALLIDA GENOMICS, INC.Inventor: Radoje DRMANAC
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Patent number: 7582431Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: GrantFiled: November 12, 2004Date of Patent: September 1, 2009Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Patent number: 7230093Abstract: The conditions under which oligonucleotide probes hybridize preferentially with entirely complementary and homologous nucleic acid targets are described. Using these hybridization conditions, overlapping oligonucleotide probes associate with a target nucleic acid. Following washes, positive hybridization signals are used to assemble the sequence of a given nucleic acid fragment. Representative target nucleic acids are applied as dots. Up to to 100,000 probes of the type (A,T,C,G)(A,T,C,G)NB(A,T,C,G) are used to determine sequence information by simultaneous hybridization with nucleic acid molecules bound to a filter. Additional hybridization conditions are provided that allow stringent hybridization of 6–10 nucleotide long oligomers which extends the utility of the invention. A computer process determines the information sequence of the target nucleic acid which can include targets with the complexity of mammalian genomes.Type: GrantFiled: January 12, 2004Date of Patent: June 12, 2007Assignee: Callida Genomics, Inc.Inventors: Radoje T. Drmanac, Radornir Crkvenjakov
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Publication number: 20060100787Abstract: Methods for making nanocodes that can be detected using scanning probe microscopy are provided, as are nanocodes constructed of two or more polymers, including homogeneous polymers such as nucleic acid molecules and heterogeneous polymers such as peptide nucleic acid polymers, and subunits useful for constructing such nanocodes. Also provided are modified nanocodes such as a nanocode containing one or more linked metals such as gold or iron and/or a linked probe that can specifically bind a target molecule. In addition, systems are provided that include such nanocodes, for example, a system that includes the nanocode and a surface and/or a scanning probe microscope probe. Methods of using such nanocodes, for example, to detect and/or identify a target molecule in a sample (e.g., a biological or environmental sample) using scanning probe microscopy, also are provided.Type: ApplicationFiled: November 9, 2004Publication date: May 11, 2006Applicants: Intel Corporation, Callida Genomics, Inc.Inventors: Andrew Berlin, Joseph Kosmoski, Narayanan Sundararajan, Xing Su, Mineo Yamakawa
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Publication number: 20050191656Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: ApplicationFiled: November 12, 2004Publication date: September 1, 2005Applicant: CALLIDA GENOMICS, INC.Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Patent number: 6864052Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: GrantFiled: January 6, 2000Date of Patent: March 8, 2005Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu