Patents by Inventor Hatim Allawi

Hatim Allawi 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).

  • Publication number: 20210404015
    Abstract: A method of sample analysis is provided. In certain embodiments, the method involves: a) amplifying a product from a sample that comprises both wild type copies of a genomic locus and mutant copies of the genomic locus that have a point mutation relative to said wild type copies of the genomic locus, to produce an amplified sample, where: i. the amplifying is done using a first primer and a second primer; and ii. the first primer comprises a 3? terminal nucleotide that base pairs with the point mutation and also comprises a nucleotide sequence that is fully complementary to a sequence in the locus with the exception of a single base mismatch within 6 bases of the 3? terminal nucleotide; and b) detecting the presence of said product in said amplified sample using a flap assay that employs an invasive oligonucleotide. A kit for performing the method is also provided.
    Type: Application
    Filed: July 8, 2021
    Publication date: December 30, 2021
    Inventors: Hongzhi Zou, Graham P. Lidgard, Michael J. Domanico, Hatim Allawi
  • Publication number: 20210262042
    Abstract: Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.
    Type: Application
    Filed: May 7, 2021
    Publication date: August 26, 2021
    Inventors: Hatim Allawi, Graham P. Lidgard, Maria Giakoumopoulos, David A. Ahlquist, William R. Taylor, Douglas Mahoney
  • Patent number: 11091812
    Abstract: A method of sample analysis is provided. In certain embodiments, the method involves: a) amplifying a product from a sample that comprises both wild type copies of a genomic locus and mutant copies of the genomic locus that have a point mutation relative to said wild type copies of the genomic locus, to produce an amplified sample, where: i. the amplifying is done using a first primer and a second primer; and ii. the first primer comprises a 3? terminal nucleotide that base pairs with the point mutation and also comprises a nucleotide sequence that is fully complementary to a sequence in the locus with the exception of a single base mismatch within 6 bases of the 3? terminal nucleotide; and b) detecting the presence of said product in said amplified sample using a flap assay that employs an invasive oligonucleotide. A kit for performing the method is also provided.
    Type: Grant
    Filed: September 12, 2019
    Date of Patent: August 17, 2021
    Assignee: EXACT SCIENCES DEVELOPMENT COMPANY, LLC
    Inventors: Hongzhi Zou, Graham P. Lidgard, Michael J. Domanico, Hatim Allawi
  • Publication number: 20210222255
    Abstract: A method for detecting a methylated genomic locus is provided. In certain embodiments, the method comprises: a) treating a nucleic acid sample that contains both unmethylated and methylated copies of a genomic locus with an agent that modifies cytosine to uracil to produce a treated nucleic acid; b) amplifying a product from the treated nucleic acid using a first primer and a second primer, wherein the first primer hybridizes to a site in the locus that contain methylcytosines and the amplifying preferentially amplifies the methylated copies of the genomic locus, to produce an amplified sample; and c) detecting the presence of amplified methylated copies of the genomic locus in the amplified sample using a flap assay that employs an invasive oligonucleotide having a 3? terminal G or C nucleotide that corresponds to a site of methylation in the genomic locus.
    Type: Application
    Filed: February 8, 2021
    Publication date: July 22, 2021
    Inventors: Graham P. Lidgard, Michael J. Domanico, Hatim Allawi, Hongzhi Zou
  • Publication number: 20210189462
    Abstract: Provided herein is technology relating to the amplification-based detection of nucleic acids and particularly, but not exclusively, to methods and compositions for minimizing variability in the activity between different samples or manufacturing lots of DNA polymerases, such as Taq DNA polymerase.
    Type: Application
    Filed: February 11, 2021
    Publication date: June 24, 2021
    Inventors: Hatim Allawi, Rebecca Oldham-Haltom, Zubin Gagrat, Michael Domanico, Graham Lidgard
  • Publication number: 20210172023
    Abstract: The present invention provides synthetic DNA strands that find use as controls or in nucleic acid testing methods. In particular, provided herein are synthetic DNA strands of known composition for use as control molecules in stool DNA testing, e.g., of mutations and/or methylation of DNA isolated from stool samples.
    Type: Application
    Filed: December 3, 2020
    Publication date: June 10, 2021
    Inventors: Ilse A. Tyler, Keith Yaeger, Michael J. Domanico, Hatim Allawi, Graham P. Lidgard
  • Patent number: 11028447
    Abstract: Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.
    Type: Grant
    Filed: July 2, 2019
    Date of Patent: June 8, 2021
    Inventors: Hatim Allawi, Graham P. Lidgard, Maria Giakoumopoulos, David A. Ahlquist, William R. Taylor, Douglas Mahoney
  • Publication number: 20210155993
    Abstract: Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.
    Type: Application
    Filed: October 23, 2020
    Publication date: May 27, 2021
    Inventors: Hatim Allawi, Graham P. Lidgard, Chateen Krueger, Michael W. Kaiser, Tamara J. Sander
  • Patent number: 10954556
    Abstract: Provided herein is technology relating to the amplification-based detection of nucleic acids and particularly, but not exclusively, to methods and compositions for minimizing variability in the activity between different samples or manufacturing lots of DNA polymerases, such as Taq DNA polymerase.
    Type: Grant
    Filed: September 18, 2018
    Date of Patent: March 23, 2021
    Inventors: Hatim Allawi, Rebecca Oldham-Haltom, Zubin Gagrat, Michael Domanico, Graham Lidgard
  • Publication number: 20210079451
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Application
    Filed: September 24, 2020
    Publication date: March 18, 2021
    Inventors: Hatim Allawi, Graham P. Lidgard, Brian Aizenstein, Tamara J. Sander, Maria Giakoumopoulos, Michael W. Kaiser, Melissa M. Gray, Abram Michael Vaccaro
  • Patent number: 10889867
    Abstract: The present invention provides synthetic DNA strands that find use as controls or in nucleic acid testing methods. In particular, provided herein are synthetic DNA strands of known composition for use as control molecules in stool DNA testing, e.g., of mutations and/or methylation of DNA isolated from stool samples.
    Type: Grant
    Filed: October 23, 2018
    Date of Patent: January 12, 2021
    Inventors: Ilse A. Tyler, Keith Yaeger, Michael J. Domanico, Hatim Allawi, Graham P. Lidgard
  • Patent number: 10822638
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Grant
    Filed: October 26, 2016
    Date of Patent: November 3, 2020
    Assignee: Exact Sciences Development Company, LLC
    Inventors: Hatim Allawi, Graham P. Lidgard, Brian Aizenstein, Tamara J. Sander, Maria Giakoumopoulos, Michael W. Kaiser, Melissa M. Gray, Abram Michael Vaccaro
  • Publication number: 20200291458
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Application
    Filed: May 29, 2020
    Publication date: September 17, 2020
    Inventors: Graham P. Lidgard, Hatim Allawi
  • Publication number: 20200291459
    Abstract: Provided herein is technology related to the chemical modification and purification of DNA. Specifically, the technology provides methods for performing a bisulfite conversion reaction on small amounts of single-stranded, fragmented DNA and performing the subsequent desulfonation and purification steps on magnetic beads.
    Type: Application
    Filed: May 29, 2020
    Publication date: September 17, 2020
    Inventors: Michael J. Domanico, Hatim Allawi, Graham P. Lidgard, Brian Aizenstein, Oliver Hunt, Tobias Charles Zutz
  • Publication number: 20200270706
    Abstract: Provided herein is reagent mixture comprising multiplexed amplification reagents and flap assay reagents for detecting, in a single reaction, mutant copies of the KRAS gene that contain any of the 34A, 34C, 34T, 35A, 35C, 35T or 38A point mutations. Methods that employ the reagent mix and kits for performing the same are also provided.
    Type: Application
    Filed: March 10, 2020
    Publication date: August 27, 2020
    Inventors: Rebecca Oldham-Haltom, Hatim Allawi, Hongzhi Zou, Michael J. Domanico, Graham P. Lidgard
  • Publication number: 20200248245
    Abstract: A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.
    Type: Application
    Filed: February 12, 2020
    Publication date: August 6, 2020
    Inventors: Rebecca Oldham-Haltom, Hongzhi Zou, Graham P. Lidgard, Michael J. Domanico, Hatim Allawi
  • Patent number: 10704081
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Grant
    Filed: October 26, 2016
    Date of Patent: July 7, 2020
    Assignee: EXACT SCIENCES DEVELOPMENT COMPANY, LLC
    Inventors: Graham P. Lidgard, Hatim Allawi
  • Patent number: 10704083
    Abstract: Provided herein is technology related to the chemical modification and purification of DNA. Specifically, the technology provides methods for performing a bisulfite conversion reaction on small amounts of single-stranded, fragmented DNA and performing the subsequent desulfonation and purification steps on magnetic beads.
    Type: Grant
    Filed: October 18, 2018
    Date of Patent: July 7, 2020
    Assignee: Exact Sciences Development Company, LLC
    Inventors: Michael J. Domanico, Hatim Allawi, Graham P. Lidgard, Brian Aizenstein, Oliver Hunt, Tobias Charles Zutz
  • Patent number: 10626465
    Abstract: Provided herein is reagent mixture comprising multiplexed amplification reagents and flap assay reagents for detecting, in a single reaction, mutant copies of the KRAS gene that contain any of the 34A, 34C, 34T, 35A, 35C, 35T or 38A point mutations. Methods that employ the reagent mix and kits for performing the same are also provided.
    Type: Grant
    Filed: August 27, 2018
    Date of Patent: April 21, 2020
    Assignee: EXACT SCIENCES DEVELOPMENT COMPANY, LLC
    Inventors: Rebecca Oldham-Haltom, Hatim Allawi, Hongzhi Zou, Michael J. Domanico, Graham P. Lidgard
  • Patent number: 10604793
    Abstract: A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: March 31, 2020
    Assignee: EXACT SCIENCES DEVELOPMENT COMPANY, LLC
    Inventors: Rebecca Oldham-Haltom, Hongzhi Zou, Graham P. Lidgard, Michael J. Domanico, Hatim Allawi