Patents by Inventor Snezana Drmanac
Snezana Drmanac 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: 20090137414Abstract: 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: October 31, 2007Publication date: May 28, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20090137404Abstract: 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: October 31, 2007Publication date: May 28, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20090118488Abstract: 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: ApplicationFiled: October 31, 2007Publication date: May 7, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20090111115Abstract: The present invention provides a sequence interrogation chemistry that combines the accuracy and haplotype integrity of long-read sequencing with improved methods of preparing genomic nucleic acids and analyzing sequence information generated from those nucleic acids. The present invention encompasses compositions comprising decorated nucleic acids stretched on substrates. The present invention further encompasses methods of making stretched decorated nucleic acids and methods of using decorated nucleic acids to obtain sequence information.Type: ApplicationFiled: October 15, 2008Publication date: April 30, 2009Applicant: COMPLETE GENOMICS, INC.Inventors: Radoje Drmanac, Snezana Drmanac
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Publication number: 20090011943Abstract: 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: ApplicationFiled: October 31, 2007Publication date: January 8, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20090005252Abstract: 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: ApplicationFiled: October 31, 2007Publication date: January 1, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20080234136Abstract: 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: October 31, 2007Publication date: September 25, 2008Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20070099208Abstract: 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: June 13, 2006Publication date: May 3, 2007Inventors: Radoje Drmanac, Matthew Callow, Snezana Drmanac, Brian Hauser, George Yeung
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Patent number: 7122373Abstract: This invention relates to novel human polynucleotides and variants thereof, their encoded polypeptides and variants thereof, to genes corresponding to these polynucleotides and to proteins expressed by the genes. The invention also relates to diagnostic and therapeutic agents employing such novel human polynucleotides, their corresponding genes or gene products, e.g., these genes and proteins, including probes, antisense constructs, and antibodies.Type: GrantFiled: May 13, 1999Date of Patent: October 17, 2006Assignee: Nuvelo, Inc.Inventors: Lewis T. Williams, Jaime Escobedo, Michael A. Innis, Pablo Dominguez Garcia, Julie Sudduth-Klinger, Christoph Reinhard, Klaus Giese, Filippo Randazzo, Giulia C. Kennedy, David Pot, Altaf Kassam, George Lamson, Radoje Drmanac, Radomir Crkvenjakov, Mark Dickson, Snezana Drmanac, Ivan Labat, Dena Leshkowitz, David Kita, Veronica Garcia, Lee William Jones, Birgit Stache-Crain
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Patent number: 6964868Abstract: This invention relates to novel human polynucleotides and variants thereof, their encoded polypeptides and variants thereof, to genes corresponding to these polynucleotides and to proteins expressed by the genes. The invention also relates to diagnostic and therapeutic agents employing such novel human polynucleotides, their corresponding genes or gene products, e.g., these genes and proteins, including probes, antisense constructs, and antibodies.Type: GrantFiled: January 28, 1999Date of Patent: November 15, 2005Assignee: Nuvelo, Inc.Inventors: Lewis T. Williams, Jaime Escobedo, Michael A. Innis, Pablo Dominguez Garcia, Julie Sudduth-Klinger, Christoph Reinhard, Klaus Giese, Filippo Randazzo, Giulia C. Kennedy, David Pot, Altaf Kassam, George Lamson, Radoje Drmanac, Radomir Crkvenjakov, Mark Dickson, Snezana Drmanac, Ivan Labat, Dena Leshkowitz, David Kita, Veronica Garcia, Lee William Jones, Birgit Stache-Crain
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Publication number: 20050227917Abstract: The present invention provides polynucleotides, as well as polypeptides encoded thereby, that are differentially expressed in cancer cells. These polynucleotides are useful in a variety of diagnostic and therapeutic methods. The present invention further provides methods of reducing growth of cancer cells. These methods are useful for treating cancer.Type: ApplicationFiled: February 12, 2004Publication date: October 13, 2005Inventors: Lewis Williams, Jaime Escobedo, Michael Innis, Pablo Garcia, Julie Sudduth-Klinger, Christoph Reinhard, Klaus Giese, Filippo Randazzo, Giulia Kennedy, David Pot, Altaf Kassam, George Lamson, Zhijun He, Elizabeth Scott, Guozhong Zhang, Theresa May, Doreen Sakamoto, Radoje Drmanac, Radomir Crkvenjakov, Mark Dickson, Snezana Drmanac, Ivan Labat, Dena Leshkowitz, David Kita, Veronica Garcia, Lee Jones, Birgit Stache-Crain
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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
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Publication number: 20050019776Abstract: The invention relates to methods for isolating and amplifying small fragments of genomic DNA for genotyping polymorphisms in human populations.Type: ApplicationFiled: June 27, 2003Publication date: January 27, 2005Inventors: Matthew Callow, Radoje Drmanac, Snezana Drmanac
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Publication number: 20030215803Abstract: This invention relates to novel human polynucleotides and variants thereof, their encoded polypeptides and variants thereof, to genes corresponding to these polynucleotides and to proteins expressed by the genes. The invention also relates to diagnostics and therapeutics comprising such novel human polynucleotides, their corresponding genes or gene products, including probes, antisense nucleotides, and antibodies. The polynucleotides of the invention correspond to a polynucleotide comprising the sequence information of at least one of SEQ ID NOS: 1-1477. The polypeptides of the invention correspond to a polypeptide comprising the amino acid sequence information of at least one of SEQ ID NOS: 1478-1568.Type: ApplicationFiled: December 7, 2001Publication date: November 20, 2003Inventors: Pablo Dominguez Garcia, Jaime Escobedo, Altaf Kassam, George Lamson, Elizabeth Scott, Radoje Drmanac, Radomir Crkvenjakov, Mark Dickson, Snezana Drmanac, Ivan Labat, Dena Leshkowitz, David Kita, Veronica Garcia, Lee William Jones, Birgit Stache-Crain
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Publication number: 20030065156Abstract: This invention relates to novel human polynucleotides and variants thereof, their encoded polypeptides and variants thereof, to genes corresponding to these polynucleotides and to proteins expressed by the genes. The invention also relates to diagnostic and therapeutic agents employing such novel human polymucleotides, their corresponding genes or gene products, e.g., these genes and proteins, including probes, antisense constructs, and antibodies.Type: ApplicationFiled: February 15, 2002Publication date: April 3, 2003Inventors: Lewis T. Williams, Jaime Escobedo, Michael A. Innis, Pablo Dominguez Garcia, Julie Sudduth-Klinger, Christoph Reinhard, Klause Giese, Filippo Randazzo, Giulia C. Kennedy, David Pot, Atlaf Kassam, George Lamson, Radoje Drmanac, Radomir Crkvenjakov, Mark Dickson, Snezana Drmanac, Ivan Labat, Dena Leshkowitz, David Kita, Veronica Garcia, Lee William Jones, Birgit Stache-Crain
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Publication number: 20020076735Abstract: The invention provides materials and methods for determining the metastatic potential of a cell and for identifying cancerous cells by determining the presence or absence of one or more expression products of at least one gene that is differentially expressed between normal cells, nonmetastatic cells, cells of low metastatic potential, and cells of high metastatic potential.Type: ApplicationFiled: May 10, 2001Publication date: June 20, 2002Inventors: Lewis T. Williams, Jaime Escobedo, Michael A. Innis, Pablo Dominguez Garcia, Julie Sudduth-Klinger, Christoph Reinhard, Klaus Giese, Filippo Randazzo, Giulia C. Kennedy, David Pot, Altaf Kassam, George Lamson, Radoje Drmanac, Radomir Crkvenjakov, Mark Dickson, Snezana Drmanac, Ivan Labat, Dena Leshkowitz, David Kita, Veronica Garcia, Lee William Jones, Birgit Stache-Crain
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Patent number: 6383742Abstract: The present invention provides a method for detecting a target nucleic acid species including the steps of providing an array of probes affixed to a substrate and a plurality of labeled probes wherein each labeled probe is selected to have a first nucleic acid sequence which is complementary to a first portion of a target nucleic acid and wherein the nucleic acid sequence of at least one probe affixed to the substrate is complementary to a second portion of the nucleic acid sequence of the target, the second portion being adjacent to the first portion; applying a target nucleic acid to the array under suitable conditions for hybridization of probe sequences to complementary sequences; introducing a labeled probe to the array; hybridizing a probe affixed to the substrate to the target nucleic acid; hybridizing the labeled probe to the target nucleic acid; affixing the labeled probe to an adjacently hybridized probe in the array; and detecting the labeled probe affixed to the probe in the array.Type: GrantFiled: August 15, 1997Date of Patent: May 7, 2002Inventors: Radoje T. Drmanac, Snezana Drmanac
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Publication number: 20020048760Abstract: The present invention provides methods and reagents useful for a wide range of nucleic acid sequence analyses, including sequencing by hybridization.Type: ApplicationFiled: April 2, 2001Publication date: April 25, 2002Applicant: Hyseq, Inc.Inventors: Snezana Drmanac, Chongjun Xu, Xiao-Hong Qian
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Patent number: 6297006Abstract: The present invention provides a method for detecting a target nucleic acid species including the steps of providing an array of probes affixed to a substrate and a plurality of labeled probes wherein each labeled probe is selected to have a first nucleic acid sequence which is complementary to a first portion of a target nucleic acid and wherein the nucleic acid sequence of at least one probe affixed to the substrate is complementary to a second portion of the nucleic acid sequence of the target, the second portion being adjacent to the first portion; applying a target nucleic acid to the array under suitable conditions for hybridization of probe sequences to complementary sequences; introducing a labeled probe to the array; hybridizing a probe affixed to the substrate to the target nucleic acid; hybridizing the labeled probe to the target nucleic acid; affixing the labeled probe to an adjacently hybridized probe in the array; and detecting the labeled probe affixed to the probe in the array.Type: GrantFiled: March 4, 1997Date of Patent: October 2, 2001Assignee: Hyseq, Inc.Inventors: Radoje T. Drmanac, Snezana Drmanac, Aaron Hou, Brian Hauser