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US 2015/0088432 A1Published application
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.
Claims51
A method comprising:
- informationally coupling an analysis engine to a sequence database storing a nucleic acid sequence from a virus-associated tumor and a chimeric reference nucleic acid sequence;
- wherein the chimeric reference nucleic acid sequence comprises at least one viral nucleic acid sequence and a mammalian nucleic acid sequence;
- identifying, by the analysis engine, an integration of at least some of the viral nucleic acid sequence in the chimeric reference nucleic acid sequence with an allele in the nucleic acid sequence from the virus-associated tumor;
- identifying, by the analysis engine, co-amplification of the allele and the at least some of the viral nucleic acid sequence;
- and
- updating a treatment recommendation record for the virus-associated tumor once co-amplification reaches a threshold value.
3 more elements
A method 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 viral nucleic acid sequence and optionally a mammalian nucleic acid sequence;
- identifying, by the analysis engine, an integration of at least some of the nucleic acid sequence from the mammalian tissue into the viral nucleic acid sequence;
- identifying, by the analysis engine, co-amplification of an allele of the nucleic acid sequence from the mammalian tissue and at least some of the viral nucleic acid sequence;
- and
- updating a treatment recommendation record for the mammal once co-amplification reaches a threshold value.
3 more elements
A method comprising:
- informationally coupling an analysis engine to a sequence database storing a nucleic acid sequence from a cervical tumor of a patient and a chimeric reference nucleic acid sequence;
- wherein the chimeric reference nucleic acid sequence comprises matched normal nucleic acid sequence from the patient and a viral nucleic acid sequence of an HPV virus;
- identifying, by the analysis engine, an integration of at least some of the viral nucleic acid sequence in the chimeric reference nucleic acid sequence with an allele of an oncogene in the nucleic acid sequence from the cervical tumor;
- identifying, by the analysis engine, co-amplification of the allele and the at least some of the viral nucleic acid sequence;
- and
- updating a treatment recommendation record for the virus-associated tumor once co-amplification reaches a threshold value.
3 more elements
A method comprising:
- informationally coupling an editing engine to a sequence database storing a nucleic acid sequence from a mammalian tissue and a plurality of viral nucleic acid sequences from a plurality of distinct viruses;
- merging, by the editing engine, the nucleic acid sequence from the mammalian tissue with the plurality of viral nucleic acid sequences 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 viral nucleic acid sequences 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.
2 more elements
Dependencies are inferred from the claim text.