Patents by Inventor Fiona Kaper
Fiona Kaper 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: 10501786Abstract: Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.Type: GrantFiled: May 28, 2015Date of Patent: December 10, 2019Assignee: Fluidigm CorporationInventors: Megan Anderson, Peilin Chen, Brian Fowler, Robert C. Jones, Fiona Kaper, Ronald Lebofsky, Andrew May
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Patent number: 10344318Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.Type: GrantFiled: May 9, 2017Date of Patent: July 9, 2019Assignee: FLUIDIGM CORPORATIONInventors: Andrew May, Peilin Chen, Jun Wang, Fiona Kaper, Megan Anderson
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Patent number: 10262104Abstract: Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.Type: GrantFiled: October 8, 2015Date of Patent: April 16, 2019Assignee: ILLUMINA, INC.Inventors: Thomas Royce, Craig April, Fiona Kaper, Jian-Bing Fan
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Publication number: 20180355349Abstract: A method of preparing a library of tagged nucleic acid fragments including contacting a population of cells directly with a lysis reagent having one or more protease to generate a cell lysate; inactivating the protease to generate an inactivated cell lysate, and applying a transposase and a transposon end composition containing a transferred strand to the inactivated cell lysate under conditions wherein the target nucleic acid and the transposon end composition undergo a transposition reaction.Type: ApplicationFiled: June 28, 2018Publication date: December 13, 2018Applicant: Illumina, Inc.Inventors: Fiona Kaper, Gordon Cann
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Patent number: 10017759Abstract: A method of preparing a library of tagged nucleic acid fragments including contacting a population of cells directly with a lysis reagent having one or more protease to generate a cell lysate; inactivating the protease to generate an inactivated cell lysate, and applying a transposase and a transposon end composition containing a transferred strand to the inactivated cell lysate under conditions wherein the target nucleic acid and the transposon end composition undergo a transposition reaction.Type: GrantFiled: June 24, 2015Date of Patent: July 10, 2018Assignee: ILLUMINA, INC.Inventors: Fiona Kaper, Gordon Cann
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Patent number: 9840732Abstract: In certain embodiments, the invention provides methods and devices for assaying single particles in a population of particles, wherein at least two parameters are measured for each particle. One or more parameters can be measured while the particles are in the separate reaction volumes. Alternatively or in addition, one or more parameters can be measured in a later analytic step, e.g., where reactions are carried out in the separate reaction volumes and the reaction products are recovered and analyzed. In particular embodiments, one or more parameter measurements are carried out “in parallel,” i.e., essentially simultaneously in the separate reaction volumes.Type: GrantFiled: May 21, 2013Date of Patent: December 12, 2017Assignee: FLUIDIGM CORPORATIONInventors: Megan Anderson, Peilin Chen, Brian Fowler, Fiona Kaper, Ronald Lebofsky, Andrew May
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Publication number: 20170349934Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.Type: ApplicationFiled: May 9, 2017Publication date: December 7, 2017Inventors: Andrew May, Peilin Chen, Jun Wang, Fiona Kaper, Megan Anderson
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Patent number: 9677119Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.Type: GrantFiled: February 13, 2014Date of Patent: June 13, 2017Assignee: Fluidigm CorporationInventors: Andrew May, Peilin Chen, Jun Wang, Fiona Kaper, Megan Anderson
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Publication number: 20170044525Abstract: Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and/or beads bearing unique barcodes such as unique molecular barcodes (UMI).Type: ApplicationFiled: April 28, 2015Publication date: February 16, 2017Inventors: Fiona KAPER, Jian-Bing FAN, Neeraj SALATHIA, Gordon M. CANN, Arash JAMSHIDI, Alex ARAVANIS
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Publication number: 20160208322Abstract: Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.Type: ApplicationFiled: May 28, 2015Publication date: July 21, 2016Inventors: Megan Anderson, Peilin Chen, Brian Fowler, Robert C. Jones, Fiona Kaper, Ronald Lebofsky, Andrew May
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Publication number: 20160098518Abstract: Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.Type: ApplicationFiled: October 8, 2015Publication date: April 7, 2016Applicant: ILLUMINA, INC.Inventors: Thomas Royce, Craig April, Fiona Kaper, Jian-Bing Fan
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Publication number: 20150376608Abstract: A method of preparing a library of tagged nucleic acid fragments including contacting a population of cells directly with a lysis reagent having one or more protease to generate a cell lysate; inactivating the protease to generate an inactivated cell lysate, and applying a transposase and a transposon end composition containing a transferred strand to the inactivated cell lysate under conditions wherein the target nucleic acid and the transposon end composition undergo a transposition reaction.Type: ApplicationFiled: June 24, 2015Publication date: December 31, 2015Inventors: Fiona Kaper, Gordon Cann
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Publication number: 20150360193Abstract: The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.Type: ApplicationFiled: February 21, 2013Publication date: December 17, 2015Applicant: Illumina, Inc.Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
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Patent number: 9181583Abstract: Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.Type: GrantFiled: March 8, 2013Date of Patent: November 10, 2015Assignee: Illumina, Inc.Inventors: Thomas Royce, Craig April, Fiona Kaper, Jian-Bing Fan
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Patent number: 9074204Abstract: Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.Type: GrantFiled: May 21, 2012Date of Patent: July 7, 2015Assignee: Fluidigm CorporationInventors: Megan Anderson, Peilin Chen, Brian Fowler, Robert C. Jones, Fiona Kaper, Ronald Lebofsky, Andrew May
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Publication number: 20140272952Abstract: In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.Type: ApplicationFiled: February 13, 2014Publication date: September 18, 2014Applicant: FLUIDIGM CORPORATIONInventors: Andrew May, Peilin Chen, Jun Wang, Fiona Kaper, Megan Anderson
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Publication number: 20140114579Abstract: Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.Type: ApplicationFiled: March 8, 2013Publication date: April 24, 2014Applicant: ILLUMINA, INC.Inventors: Thomas Royce, Craig April, Fiona Kaper, Jian-Bing Fan
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Patent number: 8691509Abstract: In certain embodiments, the invention provides amplification methods in which nucleotide tag(s) and a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.Type: GrantFiled: April 2, 2010Date of Patent: April 8, 2014Assignee: Fluidigm CorporationInventors: Andrew May, Peilin Chen, Jun Wang, Fiona Kaper, Megan Anderson
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Publication number: 20140045706Abstract: Embodiments of the present disclosure provide methods and systems for determining the haplotype of a biological sample. Particular embodiments provide methods for long range haplotyping of a genome.Type: ApplicationFiled: February 24, 2012Publication date: February 13, 2014Applicant: ILLUMINA, INC.Inventors: Jian-Bing Fan, Jeffrey S. Fisher, Fiona Kaper
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Publication number: 20130323732Abstract: In certain embodiments, the invention provides methods and devices for assaying single particles in a population of particles, wherein at least two parameters are measured for each particle. One or more parameters can be measured while the particles are in the separate reaction volumes. Alternatively or in addition, one or more parameters can be measured in a later analytic step, e.g., where reactions are carried out in the separate reaction volumes and the reaction products are recovered and analyzed. In particular embodiments, one or more parameter measurements are carried out “in parallel,” i.e., essentially simultaneously in the separate reaction volumes.Type: ApplicationFiled: May 21, 2013Publication date: December 5, 2013Applicant: Fluidigm CorporationInventors: Megan Anderson, Peilin Chen, Brian Fowler, Fiona Kaper, Ronald Lebofsky, Andrew May