Patents by Inventor Elizabeth Patricia St. John

Elizabeth Patricia St. John 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).

  • System and method for detection of HIV tropism variants
    Patent number: 8344123
    Abstract: An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is described that comprises the steps of: generating cDNA species from each RNA molecule in an HIV sample population; amplifying at least one first amplicon from the cDNA species, wherein each first amplicon comprises a plurality of amplified copies and is amplified with a pair of nucleic acid primers that define a locus of the first amplicon; clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons wherein a plurality of the second amplicons comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition of the substantially identical copies from at least 100 of the immobilized populations in parallel on a single substrate; and detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic ac
    Type: Grant
    Filed: December 16, 2010
    Date of Patent: January 1, 2013
    Assignee: 454 Life Sciences Corporation
    Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
  • SYSTEM AND METHOD FOR DETECTION OF HIV-1 CLADES AND RECOMBINANTS OF THE REVERSE TRANSCRIPTASE AND PROTEASE REGIONS
    Publication number: 20120322665
    Abstract: A method for detecting low frequency occurrence of one or more HIV sequence variants associated with reverse transcriptase and/or protease is described that comprises the steps of: (a) generating a cDNA species from a plurality of RNA molecules in an HIV sample population; (b) amplifying a plurality of first amplicons from the cDNA species, wherein each first amplicon is amplified with a pair of nucleic acid primers capable of generating amplicons from an HIV clade comprising clade A, clade B, clade C, clade D, clade F, and clade G; (c) clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons; (d) determining a nucleic acid sequence composition of the second amplicons; and (e) detecting one or more sequence variants in the nucleic acid sequence composition of the second amplicons.
    Type: Application
    Filed: September 28, 2011
    Publication date: December 20, 2012
    Applicant: 454 Life Sciences Corporation
    Inventors: Elizabeth Patricia St. John, Birgitte Binderup Simen
  • SYSTEM AND METHOD FOR DETECTION OF HIV TROPISM VARIANTS
    Publication number: 20110165556
    Abstract: An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is described that comprises the steps of: generating cDNA species from each RNA molecule in an HIV sample population; amplifying at least one first amplicon from the cDNA species, wherein each first amplicon comprises a plurality of amplified copies and is amplified with a pair of nucleic acid primers that define a locus of the first amplicon; clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons wherein a plurality of the second amplicons comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition of the substantially identical copies from at least 100 of the immobilized populations in parallel on a single substrate; and detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic ac
    Type: Application
    Filed: December 16, 2010
    Publication date: July 7, 2011
    Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
  • System and method for detection of HIV tropism variants
    Patent number: 7888034
    Abstract: An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is described that comprises the steps of: generating cDNA species from each RNA molecule in an HIV sample population; amplifying at least one first amplicon from the cDNA species, wherein each first amplicon comprises a plurality of amplified copies and is amplified with a pair of nucleic acid primers that define a locus of the first amplicon; clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons wherein a plurality of the second amplicons comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition of the substantially identical copies from at least 100 of the immobilized populations in parallel on a single substrate; and detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic ac
    Type: Grant
    Filed: June 17, 2009
    Date of Patent: February 15, 2011
    Assignee: 454 Life Sciences Corporation
    Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
  • System and method for detection of HIV integrase variants
    Publication number: 20100136516
    Abstract: An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with integrase is described that comprises the steps of: (a) generating a cDNA species from a plurality of RNA molecules in an HIV sample population; (b) amplifying a plurality of first amplicons from the cDNA species, wherein each first amplicon is amplified with a pair of nucleic acid primers; (c) clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons; (d) determining a nucleic acid sequence composition of the second amplicons; (e) detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic acid sequence composition of the second amplicons; and (f) correlating the detected sequence variants with variation associated with HIV integrase.
    Type: Application
    Filed: November 19, 2009
    Publication date: June 3, 2010
    Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
  • System and method for detection of HIV tropism variants
    Publication number: 20100003687
    Abstract: An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is described that comprises the steps of: generating cDNA species from each RNA molecule in an HIV sample population; amplifying at least one first amplicon from the cDNA species, wherein each first amplicon comprises a plurality of amplified copies and is amplified with a pair of nucleic acid primers that define a locus of the first amplicon; clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons wherein a plurality of the second amplicons comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition of the substantially identical copies from at least 100 of the immobilized populations in parallel on a single substrate; and detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic ac
    Type: Application
    Filed: June 17, 2009
    Publication date: January 7, 2010
    Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
  • System and method for detection of HIV tropism variants
    Patent number: RE46293
    Abstract: An embodiment of a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is described that comprises the steps of: generating cDNA species from each RNA molecule in an HIV sample population; amplifying at least one first amplicon from the cDNA species, wherein each first amplicon comprises a plurality of amplified copies and is amplified with a pair of nucleic acid primers that define a locus of the first amplicon; clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons wherein a plurality of the second amplicons comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition of the substantially identical copies from at least 100 of the immobilized populations in parallel on a single substrate; and detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic ac
    Type: Grant
    Filed: December 30, 2014
    Date of Patent: January 31, 2017
    Assignee: 454 Life Sciences Corporation
    Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John