Patents by Inventor Varun BAGAI

Varun BAGAI 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: 20250084470
    Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.
    Type: Application
    Filed: September 25, 2024
    Publication date: March 13, 2025
    Inventors: Rajesh Gottimukkala, Amir Marcovitz, Jeoffrey Schageman, Varun Bagai, Jian Gu, James Veitch, Kelli Bramlett, Scott Myrand, Fiona Hyland, Seth Sadis, Paul Williams
  • Patent number: 12139753
    Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.
    Type: Grant
    Filed: March 20, 2020
    Date of Patent: November 12, 2024
    Assignee: Life Technologies Corporation
    Inventors: Rajesh Gottimukkala, Amir Marcovitz, Jeoffrey Schageman, Varun Bagai, Jian Gu, James Veitch, Kelli Bramlett, Scott Myrand, Fiona Hyland, Seth Sadis, Paul Williams
  • Publication number: 20240203525
    Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.
    Type: Application
    Filed: December 7, 2023
    Publication date: June 20, 2024
    Inventors: Rajesh Gottimukkala, Cheng-Zong Bai, Dumitru Brinza, Jeoffrey Schageman, Varun Bagai
  • Patent number: 11894105
    Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.
    Type: Grant
    Filed: September 20, 2018
    Date of Patent: February 6, 2024
    Assignee: Life Technologies Corporation
    Inventors: Rajesh Gottimukkala, Cheng-Zong Bai, Dumitru Brinza, Jeoffrey Schageman, Varun Bagai
  • Publication number: 20200318175
    Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.
    Type: Application
    Filed: March 20, 2020
    Publication date: October 8, 2020
    Inventors: Rajesh GOTTIMUKKALA, Amir MARCOVITZ, Jeoffrey SCHAGEMAN, Varun BAGAI, Jian GU, James VEITCH, Kelli BRAMLETT, Scott MYRAND, Fiona HYLAND, Seth SADIS, Paul WILLIAMS
  • Publication number: 20190087539
    Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.
    Type: Application
    Filed: September 20, 2018
    Publication date: March 21, 2019
    Inventors: Rajesh GOTTIMUKKALA, Cheng-Zong BAI, Dumitru BRINZA, Jeoffrey SCHAGEMAN, Varun BAGAI