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.
Type:
Grant
Filed:
July 11, 2018
Date of Patent:
June 14, 2022
Assignee:
Five3 Genomics, LLC
Inventors:
John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
Abstract: Systems and methods of genomic analysis are presented that provide a framework to determine a tumor's clonality, the number and proportion of all major clones, and the variants that distinguish them. Contemplated systems and methods also allow phasing mutations to parental alleles to so time their emergence within the population of tumor cells, and provide an accurate estimate of the amount of contaminating normal tissue that was present in the tumor biopsy.
Abstract: Contemplated systems and methods allow for computational genomic analysis using paired-end sequence analysis and split read refinement to thereby identify high-confidence breakpoints associated with high copy numbers and orientation of rearrangements, which is then the basis for full reconstruction of double minutes (DM). In especially preferred aspects, the DM will also include an oncogene or tumor suppressor gene, and/or may be found in blood or blood derived fluids.
Type:
Grant
Filed:
February 22, 2017
Date of Patent:
March 30, 2021
Assignee:
Five3 Genomics, LLC
Inventors:
John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz
Abstract: Contemplated systems and methods allow for computational genomic analysis using paired-end sequence analysis and split read refinement to thereby identify high-confidence breakpoints associated with high copy numbers and orientation of rearrangements, which is then the basis for full reconstruction of double minutes (DM). In especially preferred aspects, the DM will also include an oncogene or tumor suppressor gene, and/or may be found in blood or blood derived fluids.
Type:
Grant
Filed:
April 15, 2016
Date of Patent:
September 15, 2020
Assignee:
Five3 Genomics, LLC
Inventors:
John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz
Abstract: Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.
Type:
Grant
Filed:
October 24, 2018
Date of Patent:
August 4, 2020
Assignee:
Five3 Genomics, LLC
Inventors:
Charles Joseph Vaske, John Zachary Sanborn, Stephen Charles Benz
Abstract: Omics patient data are analyzed using sequences or diff objects of tumor and matched normal tissue to identify patient and disease specific mutations, using transcriptomic data to identify expression levels of the mutated genes, and pathway analysis based on the so obtained omic data to identify specific pathway characteristics for the diseased tissue. Most notably, many different tumors have shared pathway characteristics, and identification of a pathway characteristic of a tumor may thus indicate effective treatment options ordinarily not considered when tumor analysis is based on anatomical tumor type only.
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.
Abstract: Contemplated systems and methods integrate genomic/exomic data with transcriptomic data by correlating a cancer associated mutation in the genome/exome with the transcription level of the affected gene carrying the mutation, particularly where the mutation is a 3-terminal nonsense mutation.
Abstract: “Omic” digital data transport systems and methods are disclosed. The disclosed systems and methods employ a transport server that assembles a transport group larger numbers of omic output files on the basis of machine specific annotation from one or more sequencing devices and user input related to one or more attributes for the omic output files.
Type:
Grant
Filed:
November 13, 2014
Date of Patent:
January 29, 2019
Assignee:
FIVE3 GENOMICS, LLC
Inventors:
Stephen Charles Benz, John Zachary Sanborn, Charles Joseph Vaske
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.