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公开(公告)号：US20220277809A1
公开(公告)日：2022-09-01
申请号：US17739792
申请日：2022-05-09
申请人： Five3 Genomics, LLC
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：US20190392921A1
公开(公告)日：2019-12-26
申请号：US16562186
申请日：2019-09-05
申请人： Five3 Genomics, LLC
发明人： John Zachary Sanborn , Charles Joseph Vaske , Stephen Charles Benz , Shahrooz Rabizadeh , Nicole Hensley , Patrick Soon-Shiong
IPC分类号： G16B30/00
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：US10193956B2
公开(公告)日：2019-01-29
申请号：US14541068
申请日：2014-11-13
申请人： Five3 Genomics, LLC
摘要： “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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公开(公告)号：US20180322245A1
公开(公告)日：2018-11-08
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
IPC分类号： G06F19/22
CPC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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公开(公告)号：US20170159133A1
公开(公告)日：2017-06-08
申请号：US15439717
申请日：2017-02-22
申请人： Five3 Genomics, LLC
CPC分类号： C12Q1/6886 , C12Q1/6869 , C12Q2600/106 , C12Q2600/172 , G16B20/00 , G16B30/00 , G16B40/00 , G16H50/20
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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16.发明申请Systems And Methods For Learning And Identification Of Regulatory Interactions In Biological Pathways 审中-公开用于学习和识别生物学途径中的调节相互作用的系统和方法公开(公告)号：US20150262082A1
公开(公告)日：2015-09-17
申请号：US14434745
申请日：2013-10-09
申请人： FIVE3 GENOMICS, LLC
摘要： 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.
摘要翻译： 考虑的系统和方法提供机器学习和使用概率图形模型识别生物学途径中的调节相互作用，特别是用于识别调节参数之间的相互作用相关性。
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公开(公告)号：US10774384B2
公开(公告)日：2020-09-15
申请号：US15099596
申请日：2016-04-15
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：US20190124135A1
公开(公告)日：2019-04-25
申请号：US16222750
申请日：2018-12-17
申请人： Five3 Genomics, LLC
摘要： “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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公开(公告)号：US20170011167A1
公开(公告)日：2017-01-12
申请号：US15099596
申请日：2016-04-15
申请人： Five3 Genomics, LLC
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.
摘要翻译： 考虑的系统和方法允许使用配对末端序列分析和分割读取细化进行计算基因组分析，从而识别与高拷贝数和重排的取向相关联的高可信度断点，这是完全重建双分钟（DM）的基础， 。 在特别优选的方面，DM还将包括致癌基因或肿瘤抑制基因，和/或可以在血液或血液衍生的流体中发现。
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20.发明申请Systems And Methods For Comprehensive Analysis Of Molecular Profiles Across Multiple Tumor And Germline Exomes 审中-公开用于多个肿瘤和种系异常的分子谱综合分析的系统和方法公开(公告)号：US20160026752A1
公开(公告)日：2016-01-28
申请号：US14726930
申请日：2015-06-01
申请人： Five3 Genomics, LLC
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.
摘要翻译： 使用肿瘤和匹配的正常组织的序列或diff对象来分析肿瘤患者数据，以鉴定患者和疾病特异性突变，使用转录组学数据来鉴定突变基因的表达水平，以及基于如此获得的omic数据以鉴定特异性途径的途径分析 病变组织的特征。 最值得注意的是，许多不同的肿瘤具有共享的通路特征，并且鉴定肿瘤特征的途径可能表明当肿瘤分析仅基于解剖肿瘤类型时通常不被考虑的有效治疗方案。
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