Patents by Inventor Birgitte Binderup Simen
Birgitte Binderup Simen 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: 8617816Abstract: In one embodiment of the invention a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is describe that comprises generating cDNA species from RNA molecules in an HIV sample population; amplifying first amplicons from the cDNA species, wherein each amplicon comprises amplified copies and is amplified with a pair of nucleic acid primers that define a locus; clonally amplifying the amplified copies of the first amplicons to produce second amplicons that comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition from at least 100 of the immobilized populations in parallel on a single instrument; detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic acid sequence composition of the at least 100 immobilized populations; and correlating the detected sequence variants with variation associated with HIVType: GrantFiled: March 14, 2008Date of Patent: December 31, 2013Assignee: 454 Life Sciences, A Roche CompanyInventors: Birgitte Binderup Simen, Christine Lubeski, Jan Fredrik Simons
-
Patent number: 8501409Abstract: In one embodiment of the invention a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is describe that comprises generating cDNA species from RNA molecules in an HIV sample population; amplifying first amplicons from the cDNA species, wherein each amplicon comprises amplified copies and is amplified with a pair of nucleic acid primers that define a locus; clonally amplifying the amplified copies of the first amplicons to produce second amplicons that comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition from at least 100 of the immobilized populations in parallel on a single instrument; detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic acid sequence composition of the at least 100 immobilized populations; and correlating the detected sequence variants with variation associated with HIVType: GrantFiled: March 14, 2008Date of Patent: August 6, 2013Assignee: 454 Life SciencesInventors: Birgitte Binderup Simen, Christine Lubeski, Jan Fredrik Simons
-
Patent number: 8344123Abstract: 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 acType: GrantFiled: December 16, 2010Date of Patent: January 1, 2013Assignee: 454 Life Sciences CorporationInventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
-
Publication number: 20120322665Abstract: 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: ApplicationFiled: September 28, 2011Publication date: December 20, 2012Applicant: 454 Life Sciences CorporationInventors: Elizabeth Patricia St. John, Birgitte Binderup Simen
-
Publication number: 20110165556Abstract: 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 acType: ApplicationFiled: December 16, 2010Publication date: July 7, 2011Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
-
Patent number: 7888034Abstract: 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 acType: GrantFiled: June 17, 2009Date of Patent: February 15, 2011Assignee: 454 Life Sciences CorporationInventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
-
Publication number: 20100203497Abstract: In one embodiment of the invention a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is describe that comprises generating cDNA species from RNA molecules in an HIV sample population; amplifying first amplicons from the cDNA species, wherein each amplicon comprises amplified copies and is amplified with a pair of nucleic acid primers that define a locus; clonally amplifying the amplified copies of the first amplicons to produce second amplicons that comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition from at least 100 of the immobilized populations in parallel on a single instrument; detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic acid sequence composition of the at least 100 immobilized populations; and correlating the detected sequence variants with variation associated with HIVType: ApplicationFiled: March 14, 2008Publication date: August 12, 2010Inventors: Birgitte Binderup Simen, Christine Lubeski, Jan Fredrik Simons
-
Publication number: 20100136516Abstract: 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: ApplicationFiled: November 19, 2009Publication date: June 3, 2010Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
-
Publication number: 20100003687Abstract: 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 acType: ApplicationFiled: June 17, 2009Publication date: January 7, 2010Inventors: Birgitte Binderup Simen, Elizabeth Patricia St. John
-
Patent number: RE46293Abstract: 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 acType: GrantFiled: December 30, 2014Date of Patent: January 31, 2017Assignee: 454 Life Sciences CorporationInventors: Birgitte Binderup Simen, Elizabeth Patricia St. John