Systems, methods, and compositions for viral-associated tumors
AssigneesFive3 Genomics, LLC, Nant Holdings IP, LLC
InventorsJohn Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
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Abstract
Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.
Claims19
A method of identifying at least one of presence and integration of a nucleic acid of a pathogen in a nucleic acid sequence of a mammalian tissue, comprising:
- informationally coupling an analysis engine to a sequence database storing a nucleic acid sequence from a mammalian tissue and a chimeric reference nucleic acid sequence;
- wherein the chimeric reference nucleic acid sequence comprises at least one nucleic acid sequence of at least one pathogen and optionally a mammalian nucleic acid sequence;
- and
- aligning the chimeric reference nucleic acid sequence and the nucleic acid sequence from the mammalian tissue, using incremental synchronized alignment, by the analysis engine, to identify at least one of presence and integration of the nucleic acid sequence of the pathogen in the nucleic acid sequence from the mammalian tissue.
A method of generating a chimeric reference nucleic acid sequence, comprising:
- informationally coupling an editing engine to a sequence database storing a nucleic acid sequence from a mammalian tissue and a plurality of nucleic acid sequences from a plurality of respective distinct pathogens;
- merging, by the editing engine, the nucleic acid sequence from the mammalian tissue with the plurality of nucleic acid sequences from the pathogens into a single chimeric nucleic acid sequence file;
- wherein the nucleic acid sequence from the mammalian tissue is organized in the single chimeric nucleic acid sequence file following a chromosomal structure, and wherein each of the plurality of nucleic acid sequences from the pathogens is organized in the single chimeric nucleic acid sequence file as a single chromosome;
- and
- updating the sequence database with the single chimeric genomic file.
Dependencies are inferred from the claim text.