LLC Five3 Genomics

Santa Cruz, CA, United States

LLC Five3 Genomics

Santa Cruz, CA, United States
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Patent
Five3 Genomics LLC | Date: 2017-02-22

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.


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.


Patent
Five3 Genomics LLC and Nant Holdings IP LLC | Date: 2014-09-26

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.


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.


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.


Patent
Five3 Genomics Llc | Date: 2014-05-28

Systems and methods are presented in which omics data from multiple cell or tissue samples are used to identify pathway elements that are associated with a treatment parameter of the cell or tissue (e.g., resistance towards a specific drug). So identified pathway elements are then modulated in silico in a statistical factor graph model to provide a modified data set that is re-evaluated with respect to the treatment parameter. Such systems and models are particularly useful for recommendation of multi-drug treatments for treatment-nave patients.


Patent
Five3 Genomics Llc | Date: 2014-04-17

Systems and methods of genomic analysis are presented that provide a framework to determine a tumors 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.


Contemplated systems and methods provide for machine learning and identification of regulatory interactions in biological pathways using a probabilistic graphical model, and especially for identification of interaction correlations among the regulatory parameters.


Patent
Five3 Genomics LLC | Date: 2016-04-15

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.


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.

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