Patents by Inventor Charles Scafe

Charles Scafe 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).

  • METHODS FOR DETECTING GENE LEVEL COPY NUMBER VARIATION IN BRCA1 AND BRCA2
    Publication number: 20250354221
    Abstract: Methods and systems for detecting gene level copy numbers for BRCA1 and BRCA2 genes include amplifying a nucleic acid sample in a presence of a primer pool to produce a plurality of amplicons. The primer pool may include target-specific primers targeting regions of exons of the BRCA1 and BRCA2 genes and sample ID regions. Overlapping amplicons cover the exons of the BRCA1 and BRCA2 genes. Sample ID amplicons are generated for targeted sample ID regions. The amplicons are sequenced to produce sequence reads. The sequence reads are mapped to a reference genome. Determining whole gene copy numbers for the BRCA1 and BRCA2 genes is based on the number of reads per amplicon for the amplicons associated with the exons of the BRCA1 and BRCA2 genes, respectively, and the number of reads per amplicon for the sample ID amplicons associated with the sample ID regions.
    Type: Application
    Filed: July 29, 2025
    Publication date: November 20, 2025
    Inventors: Charles Scafe, Fiona Hyland
  • METHODS AND SYSTEMS TO DETECT LARGE REARRANGEMENTS IN BRCA1/2
    Publication number: 20240035094
    Abstract: A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.
    Type: Application
    Filed: August 8, 2023
    Publication date: February 1, 2024
    Inventors: Charles SCAFE, Dumitru BRINZA, James VEITCH, Rongsu QI, Fiona HYLAND
  • METHODS AND SYSTEMS TO DETECT LARGE REARRANGEMENTS IN BRCA1/2
    Publication number: 20180340234
    Abstract: A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.
    Type: Application
    Filed: May 25, 2018
    Publication date: November 29, 2018
    Inventors: Charles Scafe, Dumitru Brinza, James Veitch, Rongsu Qi, Fiona Hyland
  • Universal-tagged oligonucleotide primers and methods of use
    Publication number: 20070128654
    Abstract: The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.
    Type: Application
    Filed: January 18, 2007
    Publication date: June 7, 2007
    Inventors: Kai Lao, Caifu Chen, Ryan Koehler, Charles Scafe, Gary Schroth
  • Universal-tagged oligonucleotide primers and methods of use
    Patent number: 7176002
    Abstract: The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.
    Type: Grant
    Filed: May 16, 2002
    Date of Patent: February 13, 2007
    Assignee: Applera Corporation
    Inventors: Kai Qin Lao, Caifu Chen, Ryan T. Koehler, Charles Scafe, Gary Schroth
  • Methods of validating snps and compiling libraries of assays
    Publication number: 20050282162
    Abstract: Libraries of assays and methods of compiling the libraries are provided. The assays can identify Single Nucleotide Polymorphisms (SNPs). Methods of validating SNPs are provided. Methods of constructing linkage disequilibrium maps using sets or subsets of SNPs are also provided.
    Type: Application
    Filed: January 27, 2003
    Publication date: December 22, 2005
    Inventors: Francisco De La Vega, Janet Ziegle, Hadar Isaac, Charles Scafe, Eugene Spier
  • Universal-tagged oligonucleotide primers and methods of use
    Publication number: 20030219751
    Abstract: The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.
    Type: Application
    Filed: May 16, 2002
    Publication date: November 27, 2003
    Inventors: Kai Qin Lao, Caifu Chen, Ryan T. Koehler, Charles Scafe, Gary Schroth