Patents by Inventor Kevin Travers

Kevin Travers 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).

  • Patent number: 10294523
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Grant
    Filed: September 23, 2015
    Date of Patent: May 21, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes
  • Publication number: 20190136313
    Abstract: Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.
    Type: Application
    Filed: June 13, 2018
    Publication date: May 9, 2019
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Publication number: 20190062833
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Application
    Filed: August 21, 2018
    Publication date: February 28, 2019
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Publication number: 20180349548
    Abstract: Provided herein are methods and systems for producing a modified biological dataset by flagging or removing a nucleic acid sequence from the biological dataset that is assigned a noise-call to produce the modified biological dataset. The noise-call may be based on comparing a gene expression level, sequence information, or a combination thereof with a nucleic acid sequence of a control sample.
    Type: Application
    Filed: March 23, 2018
    Publication date: December 6, 2018
    Inventors: P. Sean Walsh, Giulia C. Kennedy, Kevin Travers, Zhanzhi Hu, Su Yeon Kim, Jing Huang
  • Patent number: 10081836
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Grant
    Filed: July 15, 2016
    Date of Patent: September 25, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Publication number: 20180211003
    Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.
    Type: Application
    Filed: January 19, 2018
    Publication date: July 26, 2018
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Patent number: 10000805
    Abstract: Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Grant
    Filed: September 20, 2016
    Date of Patent: June 19, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Patent number: 9951383
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Methods are provided that include linking forward and reverse strands of a double stranded segment to form circular template molecules, and obtaining sequence data from the circular template molecule to identify modified bases, for example including the use of bisulfite treatment. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Grant
    Filed: September 21, 2016
    Date of Patent: April 24, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Patent number: 9910956
    Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.
    Type: Grant
    Filed: August 19, 2016
    Date of Patent: March 6, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Publication number: 20180016642
    Abstract: Provided herein are methods, systems and kits for stratification of risk of disease occurrence of a sample obtained from a subject by combining two or more feature spaces to improve individualization of subject management.
    Type: Application
    Filed: September 1, 2017
    Publication date: January 18, 2018
    Inventors: Giulia C. KENNEDY, Moraima PAGAN, Chu-Fang LIN, Jing HUANG, P. Sean WALSH, Hajime MATSUZAKI, Kevin TRAVERS, Su Yeon KIM
  • Patent number: 9738929
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: December 19, 2016
    Date of Patent: August 22, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid, Cheryl Heiner, Kevin Travers
  • Publication number: 20170233802
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Application
    Filed: September 28, 2016
    Publication date: August 17, 2017
    Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Publication number: 20170107570
    Abstract: Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Application
    Filed: September 20, 2016
    Publication date: April 20, 2017
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Patent number: 9600626
    Abstract: Computer systems, computer readable media, and computer methods for obtaining, calling, and assembling nucleic acid sequences are presented. In some aspects the invention includes the sequencing of template constructs that comprise double stranded portions in partially contiguous constructs, to provide for single molecule consensus sequence determination through one or both of sequencing sense and antisense strands in the same molecule.
    Type: Grant
    Filed: March 23, 2016
    Date of Patent: March 21, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Patent number: 9582640
    Abstract: Methods obtaining a single molecule consensus sequence for a single template molecule, and for obtaining a plurality of single molecule consensus sequences for a plurality of single template molecules is provided. Template molecules having two complementary regions connected with a linker are sequenced. A single read from each template molecule can be obtained, the read containing sequence information for each of the complementary regions. Single molecule consensus sequences can be determined from these reads by comparing the sequence information of the two complementary regions.
    Type: Grant
    Filed: April 1, 2016
    Date of Patent: February 28, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Publication number: 20170037464
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Methods are provided that include linking forward and reverse strands of a double stranded segment to form circular template molecules, and obtaining sequence data from the circular template molecule to identify modified bases, for example including the use of bisulfite treatment. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Application
    Filed: September 21, 2016
    Publication date: February 9, 2017
    Inventors: Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Patent number: 9551028
    Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.
    Type: Grant
    Filed: November 25, 2014
    Date of Patent: January 24, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Keith Bjornson, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig, Stephen Turner
  • Publication number: 20170009289
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Application
    Filed: July 15, 2016
    Publication date: January 12, 2017
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Patent number: 9542527
    Abstract: Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application.
    Type: Grant
    Filed: September 25, 2014
    Date of Patent: January 10, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Publication number: 20160376647
    Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.
    Type: Application
    Filed: August 19, 2016
    Publication date: December 29, 2016
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma