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1. 发明授权

US10793895B2 Systems and methods for epigenetic analysis 有权
公开(公告)号：US10793895B2
公开(公告)日：2020-10-06
申请号：US15007874
申请日：2016-01-27
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke , Wan-Ping Lee
IPC分类号： G01N33/48 , G01N31/00 , C12Q1/6806 , C12Q1/6874 , G16B30/00 , C12Q1/6869
摘要： The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (DAG) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the DAG to determine locations and patterns of the epigenetic modification within the genome.

2. 发明申请

US20200232029A1 SYSTEMS AND METHODS FOR MITOCHONDRIAL ANALYSIS 审中-公开
公开(公告)号：US20200232029A1
公开(公告)日：2020-07-23
申请号：US16798759
申请日：2020-02-24
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke , Piotr Szamel
IPC分类号： C12Q1/6874 , C12Q1/6888
摘要： The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.

3. 发明申请

US20200165683A1 SYSTEMS AND METHODS FOR ANALYZING CIRCULATING TUMOR DNA 审中-公开
公开(公告)号：US20200165683A1
公开(公告)日：2020-05-28
申请号：US16525822
申请日：2019-07-30
申请人： Seven Bridges Genomics Inc.
发明人： Wan-Ping Lee , Devin Locke
IPC分类号： C12Q1/6886 , G16B30/00 , G16B5/00
摘要： The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient's tumor mutation burden.

4. 发明授权

US11250931B2 Systems and methods for detecting recombination 有权
公开(公告)号：US11250931B2
公开(公告)日：2022-02-15
申请号：US15254258
申请日：2016-09-01
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke
IPC分类号： G01N33/48 , G16B20/20 , G16H50/50 , G16B20/00 , G16B30/00 , G16B30/10
摘要： A method for screening for disease in a genomic sample is includes receiving a representation of a reference genome comprising a sequence of symbols. The presence of a predicted mutational event is identified in a location of the reference genome. An alternate path is created in the reference genome representing the predicted mutational event. A plurality of sequence reads are obtained from a genomic sample, wherein at least one sequence read comprises at least a portion of the predicted mutational event. The at least one sequence read is then mapped to the reference genome and a location is determined corresponding to the predicted mutational event. The predicted mutational event is then identified as present in the genomic sample. The method may be used to detect evidence of non-allelic homologous recombination (NAHR) occurring in genomic samples.

5. 发明申请

US20170199959A1 GENETIC ANALYSIS SYSTEMS AND METHODS 审中-公开
公开(公告)号：US20170199959A1
公开(公告)日：2017-07-13
申请号：US14994758
申请日：2016-01-13
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke
IPC分类号： G06F19/14 , G06F19/22
CPC分类号： G16B30/00
摘要： Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing. The graph branches into plural paths, each defined by pointers to other fixed locations in the memory, where the genomes diverge due to either divergent homology or non-homologous portions. The graph can represent whole genomic information for multiple species with the natural relationships among parts of the genomes being represented by the structure of the graph. Newly obtained sequences such as output from NGS instruments can be mapped onto the graph for assembly or identification.

6. 发明申请

US20160364523A1 SYSTEMS AND METHODS FOR IDENTIFYING MICROORGANISMS 审中-公开
标题翻译：用于识别微生物的系统和方法
公开(公告)号：US20160364523A1
公开(公告)日：2016-12-15
申请号：US15007865
申请日：2016-01-27
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke , Piotr Szamel
IPC分类号： G06F19/22
CPC分类号： G16B30/00
摘要： The invention provides methods for identifying a microorganism by aligning sequence reads to a graph, such as a directed acyclic graph (DAG), that contains condensed sequence information of a conserved region from multiple known microorganisms. The DAG can be constructed by obtaining sequence information of known reference microorganisms. The DAG also includes the identities of the known microorganisms that correspond to particular paths. Sequence reads obtained from an unknown sample can thus be aligned to paths in the DAG using an alignment algorithm, and the identity of a microorganism in the sample can be determined based on which path in the DAG to which the sequence reads align best.
摘要翻译：本发明提供了通过将序列读取与图形（诸如有向无环图（DAG））相一致来鉴定微生物的方法，其包含来自多个已知微生物的保守区域的缩合序列信息。可以通过获得已知参考微生物的序列信息来构建DAG。 DAG还包括对应于特定路径的已知微生物的身份。因此，从未知样本获得的序列读数可以使用比对算法与DAG中的路径对齐，并且可以基于序列读取对齐最佳的DAG中的哪个路径来确定样品中的微生物的身份。

7. 发明申请

US20220254444A1 SYSTEMS AND METHODS FOR DETECTING RECOMBINATION 有权
公开(公告)号：US20220254444A1
公开(公告)日：2022-08-11
申请号：US17670380
申请日：2022-02-11
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke
IPC分类号： G16B20/20 , G16H50/50 , G16B20/00 , G16B30/00 , G16B30/10
摘要： A method for screening for disease in a genomic sample is includes receiving a representation of a reference genome comprising a sequence of symbols. The presence of a predicted mutational event is identified in a location of the reference genome. An alternate path is created in the reference genome representing the predicted mutational event. A plurality of sequence reads are obtained from a genomic sample, wherein at least one sequence read comprises at least a portion of the predicted mutational event. The at least one sequence read is then mapped to the reference genome and a location is determined corresponding to the predicted mutational event. The predicted mutational event is then identified as present in the genomic sample. The method may be used to detect evidence of non-allelic homologous recombination (NAHR) occurring in genomic samples.

8. 发明授权

US10584380B2 Systems and methods for mitochondrial analysis 有权
公开(公告)号：US10584380B2
公开(公告)日：2020-03-10
申请号：US15014483
申请日：2016-02-03
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke , Piotr Szamel
IPC分类号： G01N33/48 , G06G7/48 , C12Q1/6874 , C12Q1/6888
摘要： The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.

9. 发明申请

US20170058365A1 SYSTEMS AND METHODS FOR ANALYZING VIRAL NUCLEIC ACIDS 审中-公开
标题翻译：用于分析病毒核酸的系统和方法
公开(公告)号：US20170058365A1
公开(公告)日：2017-03-02
申请号：US15014500
申请日：2016-02-03
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke , Piotr Szamel
IPC分类号： C12Q1/70
CPC分类号： C12Q1/701 , C12Q1/6809 , C12Q1/70 , C12Q2600/156 , G16B30/00 , C12Q2537/165
摘要： The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.
摘要翻译：本发明提供了通过用有向无环图（DAG）代表病毒遗传多样性来分析病毒的系统和方法，其允许遗传测序技术检测稀有变异并且表示样品内的难以对文档的多样性。此外，当来自宿主的样品进行测序时，宿主特异性序列DAG可用于有效地将病毒核酸序列读取与宿主序列读数分离。可以使用病毒参考DAG来表示已知的病毒基因组，并且可以将来自样品的病毒序列读取与病毒DAG进行比较，以鉴定从其中导出读数的病毒种类或菌株。如果病毒序列读取表明在感染宿主的病毒中有很大的遗传多样性，那么这些读数可以被组装成DAG，其本身正好代表该多样性。

10. 发明授权

US10724110B2 Systems and methods for analyzing viral nucleic acids 有权
公开(公告)号：US10724110B2
公开(公告)日：2020-07-28
申请号：US15014500
申请日：2016-02-03
申请人： Seven Bridges Genomics Inc.
发明人： Devin Locke , Piotr Szamel
IPC分类号： G01N33/48 , C12Q1/70 , G16B30/00 , C12Q1/6809
摘要： The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.

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