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公开(公告)号：US20150261912A1
公开(公告)日：2015-09-17
申请号：US14434397
申请日：2014-04-17
申请人： FIVE3 GENOMICS, LLC
发明人： John Zachary Sanborn
CPC分类号： G16B20/00 , C12Q1/6809 , C12Q1/6886 , C12Q2600/156 , G16B30/00 , G16B40/00 , C12Q2537/165
摘要： 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.
摘要翻译： 提供了基因组分析的系统和方法，其提供了确定肿瘤的克隆性，所有主要克隆的数量和比例以及区分它们的变体的框架。 考虑的系统和方法还允许相对于亲本等位基因的相位突变，以使其在肿瘤细胞群体内出现，并提供对肿瘤活检中存在的污染正常组织的量的准确估计。
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2.发明申请Distributed System Providing Dynamic Indexing And Visualization Of Genomic Data 审中-公开分布式系统提供基因组数据的动态索引和可视化公开(公告)号：US20140368550A1
公开(公告)日：2014-12-18
申请号：US14363788
申请日：2012-12-07
申请人： Five3 Genomics, LLC
CPC分类号： G06T3/40 , G06F19/22 , G06F19/26 , G06F19/28 , G06T2200/24 , G09G5/373 , G09G2340/045 , G09G2354/00
摘要： 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.
摘要翻译： 提供了用于基因组数据的动态可视化的系统和方法，其中基因组可视化系统根据序列对象内的比例相关注释来适应信息内容的呈现。
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3.发明申请公开(公告)号：US20200185053A1
公开(公告)日：2020-06-11
申请号：US16733013
申请日：2020-01-02
发明人： Shahrooz Rabizadeh , John Zachary Sanborn , Charles Joseph Vaske , Stephen Charles Benz , Patrick Soon-Shiong
摘要： 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.
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公开(公告)号：US20190066262A1
公开(公告)日：2019-02-28
申请号：US16169946
申请日：2018-10-24
申请人： Five3 Genomics, LLC
摘要： 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.
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公开(公告)号：US10176295B2
公开(公告)日：2019-01-08
申请号：US14499023
申请日：2014-09-26
发明人： John Zachary Sanborn , Charles Joseph Vaske , Stephen Charles Benz , Shahrooz Rabizadeh , Nicole Hensley , Patrick Soon-Shiong
IPC分类号： G06F19/22
摘要： 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.
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6.发明申请Systems and Methods For RNA Analysis In Functional Confirmation Of Cancer Mutations 审中-公开用于RNA分析的系统和方法在癌症突变的功能确认中公开(公告)号：US20150278435A1
公开(公告)日：2015-10-01
申请号：US14668518
申请日：2015-03-25
申请人： Five3 Genomics, LLC
发明人： John Zachary Sanborn
摘要： 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.
摘要翻译： 考虑的系统和方法通过将基因组/外显子中的癌症相关突变与携带突变的受影响基因的转录水平相关联，特别是在突变是3末端无义突变的情况下，将基因组/外显子数据与转录组数据相结合。
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公开(公告)号：US11361844B2
公开(公告)日：2022-06-14
申请号：US16032421
申请日：2018-07-11
发明人： John Zachary Sanborn , Charles Joseph Vaske , Stephen Charles Benz , Shahrooz Rabizadeh , Nicole Hensley , Patrick Soon-Shiong
摘要： 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.
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公开(公告)号：US10961586B2
公开(公告)日：2021-03-30
申请号：US15439717
申请日：2017-02-22
申请人： Five3 Genomics, LLC
IPC分类号： C12Q1/68 , C12Q1/6886 , G16B20/00 , G16B30/00 , G16B40/00 , G16H50/20 , C12Q1/6869
摘要： 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.
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公开(公告)号：US10733701B2
公开(公告)日：2020-08-04
申请号：US16169946
申请日：2018-10-24
申请人： Five3 Genomics, LLC
摘要： 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.
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公开(公告)号：US10192027B2
公开(公告)日：2019-01-29
申请号：US14668518
申请日：2015-03-25
申请人： Five3 Genomics, LLC
发明人： John Zachary Sanborn
摘要： 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.
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