Patents by Inventor Dmitry Lyakhov
Dmitry Lyakhov 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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Patent number: 10767208Abstract: The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.Type: GrantFiled: September 6, 2012Date of Patent: September 8, 2020Assignee: GEN-PROBE INCORPORATEDInventors: Norman C. Nelson, Jijumon Chelliserry, Steven T. Brentano, Dmitry Lyakhov, Matthew C. Friedenberg, Anne-Laure Shapiro
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Patent number: 10752944Abstract: The invention provides methods of forming a circular template for sequencing a target nucleic acid. The circular template is generated by amplification of a segment of the target nucleic acid with chimeric primers with complementary 5? ends. The circular template has a single nick or gap providing a site for initiation of template-directed extension for sequence analysis. Sequencing of a single template generates reads of alternating segments of the same strand of the target nucleic spaced by primer segments. The different reads of the same strand of the target nucleic acid can be compiled to generate a consensus sequence. Because only one strand of the target nucleic acid is sequenced per reaction, the present method avoids errors introduced by unwittingly combining sequences of both strands of a heteroduplex PCR product.Type: GrantFiled: September 6, 2012Date of Patent: August 25, 2020Assignee: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, Matthew C. Friedenberg, Anne-Laure Shapiro
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Patent number: 10724085Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: GrantFiled: February 22, 2018Date of Patent: July 28, 2020Inventors: Steven T. Brentano, Dmitry Lyakhov, Norman C. Nelson, James D. Carlson, Michael M. Becker, Lyle J. Arnold, Jr.
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Patent number: 10415092Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: GrantFiled: January 27, 2017Date of Patent: September 17, 2019Assignee: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, James D. Carlson, Norman C. Nelson, Lyle J. Arnold, Michael M. Becker
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Patent number: 10407723Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: GrantFiled: May 15, 2017Date of Patent: September 10, 2019Assignee: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, James D. Carlson, Norman C. Nelson, Lyle J. Arnold, Michael M. Becker
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Patent number: 10119163Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: GrantFiled: March 2, 2016Date of Patent: November 6, 2018Assignee: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, Norman C. Nelson, James D. Carlson, Michael M. Becker, Lyle J. Arnold, Jr.
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Publication number: 20180208981Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: ApplicationFiled: February 22, 2018Publication date: July 26, 2018Inventors: Steven T. BRENTANO, Dmitry LYAKHOV, Norman C. NELSON, James D. CARLSON, Michael M. BECKER, Lyle J. ARNOLD, JR.
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Publication number: 20170342491Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: ApplicationFiled: May 15, 2017Publication date: November 30, 2017Inventors: Steven T. BRENTANO, Dmitry LYAKHOV, James D. CARLSON, Norman C. NELSON, Lyle J. ARNOLD, Michael M. BECKER
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Publication number: 20170321273Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: ApplicationFiled: January 27, 2017Publication date: November 9, 2017Inventors: Steven T. BRENTANO, Dmitry LYAKHOV, James D. CARLSON, Norman C. NELSON, Lyle J. ARNOLD, Michael M. BECKER
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Patent number: 9677135Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: GrantFiled: December 17, 2013Date of Patent: June 13, 2017Assignee: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, James D. Carlson, Norman C. Nelson, Lyle J. Arnold, Jr., Michael M. Becker
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Publication number: 20160348162Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: ApplicationFiled: March 2, 2016Publication date: December 1, 2016Inventors: Steven T. BRENTANO, Dmitry LYAKHOV, Norman C. NELSON, James D. CARLSON, Michael M. BECKER, Lyle J. ARNOLD, Jr.
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Patent number: 9399796Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: GrantFiled: July 31, 2013Date of Patent: July 26, 2016Assignee: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, Norman C. Nelson, James D. Carlson, Michael M. Becker, Lyle J. Arnold, Jr.
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Patent number: 9169512Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: GrantFiled: July 1, 2010Date of Patent: October 27, 2015Assignee: Gen-Probe IncorporatedInventors: Steven T. Brentano, Dmitry Lyakhov, James D. Carlson, Michael M. Becker, Norman C. Nelson, Lyle J. Arnold, Jr.
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Publication number: 20140378318Abstract: The invention provides methods of forming a circular template for sequencing a target nucleic acid. The circular template is generated by amplification of a segment of the target nucleic acid with chimeric primers with complementary 5? ends. The circular template has a single nick or gap providing a site for initiation of template-directed extension for sequence analysis. Sequencing of a single template generates reads of alternating segments of the same strand of the target nucleic spaced by primer segments. The different reads of the same strand of the target nucleic acid can be compiled to generate a consensus sequence. Because only one strand of the target nucleic acid is sequenced per reaction, the present method avoids errors introduced by unwittingly combining sequences of both strands of a heteroduplex PCR product.Type: ApplicationFiled: September 6, 2012Publication date: December 25, 2014Applicant: GEN-PROBE INCORPORATEDInventors: Steven T. Brentano, Dmitry Lyakhov, Matthew C. Friedenberg, Anne-Laure Shapiro
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Publication number: 20140329282Abstract: The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.Type: ApplicationFiled: September 6, 2012Publication date: November 6, 2014Applicant: GEN-PROBE INCORPORATEDInventors: Norman C. Nelson, Jijumon Chelliserry, Steven T. Brentano, Dmitry Lyakhov, Matthew C. Friedenberg, Anne-Laure Shapiro
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Publication number: 20140127700Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: ApplicationFiled: December 17, 2013Publication date: May 8, 2014Applicant: GEN-PROBE INCORPORATEDInventors: Steven T. BRENTANO, Dmitry LYAKHOV, James D. CARLSON, Norman C. NELSON, Lyle J. ARNOLD, JR., Michael M. BECKER
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Patent number: 8642268Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: GrantFiled: April 30, 2012Date of Patent: February 4, 2014Assignee: Gen-Probe IncorporatedInventors: Steven T. Brentano, Dmitry Lyakhov, James D. Carlson, Norman C. Nelson, Lyle J. Arnold, Jr., Michael M. Becker
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Publication number: 20130309673Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: ApplicationFiled: July 31, 2013Publication date: November 21, 2013Applicant: Gen-Probe IncorporatedInventors: Steven T. BRENTANO, Dmitry LYAKHOV, Norman C. NELSON, James D. CARLSON, Michael M. BECKER, Lyle J. ARNOLD, JR.
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Patent number: 8512955Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: GrantFiled: July 1, 2010Date of Patent: August 20, 2013Assignee: Gen-Probe IncorporatedInventors: Steven T. Brentano, Dmitry Lyakhov, Norman C. Nelson, James D. Carlson, Michael M. Becker, Lyle J. Arnold, Jr.
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Publication number: 20120264122Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.Type: ApplicationFiled: April 30, 2012Publication date: October 18, 2012Applicant: GEN-PROBE INCORPORATEDInventors: Steven T. BRENTANO, Dmitry LYAKHOV, James D. CARLSON, Norman C. NELSON, Lyle J. ARNOLD, JR.