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1. 发明申请

US20210257052A1 Bioinformatics Systems, Apparatuses, and Methods for Performing Secondary and/or Tertiary Processing 有权
公开(公告)号：US20210257052A1
公开(公告)日：2021-08-19
申请号：US17165900
申请日：2021-02-02
申请人： Edico Genome, Corp.
发明人： Pieter Van Rooyen , Michael Ruehle , Rami Mehio , Gavin Stone , Mark Hahm , Eric Ojard , Amnon Ptashek
IPC分类号： G16B30/00 , G16B20/00 , G16B50/00
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

2. 发明申请

US20150339437A1 DYNAMIC GENOME REFERENCE GENERATION FOR IMPROVED NGS ACCURACY AND REPRODUCIBILITY 有权
标题翻译：改进NGS精度和可重复性的动态基因参考生成
公开(公告)号：US20150339437A1
公开(公告)日：2015-11-26
申请号：US14630571
申请日：2015-02-24
申请人： Edico Genome Corporation
发明人： Robert McMillen , Michael Ruehle , John Cooper Roddey
IPC分类号： G06F19/22
CPC分类号： G06F19/22
摘要： A “dynamic” reference is presented that utilizes population level information to improve reference-based alignment to detect novel, deleterious, or functional variants in clinical sequencing applications. An automatically updated database of known genetic variants is provided to a memory connected with an integrated circuit configured for genetic sequence data with the dynamic reference and reference variants.
摘要翻译：提出了一种“动态”参考，其利用群体级别信息来改进基于参考的比对以检测临床测序应用中的新颖，有害或功能变体。将已知遗传变体的自动更新的数据库提供给与配置为具有动态参考和参考变体的遗传序列数据的集成电路连接的存储器。

3. 发明授权

US09014989B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
标题翻译：在集成电路处理平台上执行的生物信息学系统，装置和方法
公开(公告)号：US09014989B2
公开(公告)日：2015-04-21
申请号：US14180248
申请日：2014-02-13
申请人： Edico Genome Corp.
发明人： Robert McMillen , Michael Ruehle
IPC分类号： G01N33/48 , G06F19/22
CPC分类号： G06F19/22 , G06F19/28
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.
摘要翻译：用于在遗传序列数据上执行序列分析管线的系统，方法和装置包括由通过物理电互连互联的一组硬连线数字逻辑电路形成的集成电路。物理电互连之一形成与用于接收基因组数据读取的电子数据源连接的集成电路的输入。硬连线数字逻辑电路被布置为一组处理引擎，每个处理引擎由硬连线数字逻辑电路的子集形成，以在序列分析管线中对基因组数据的读取执行一个或多个步骤。硬连线数字逻辑电路的每个子集以有线配置形成，以执行序列分析流水线中的一个或多个步骤。

4. 发明申请

US20140200166A1 BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS EXECUTED ON AN INTEGRATED CIRCUIT PROCESSING PLATFORM 有权
公开(公告)号：US20140200166A1
公开(公告)日：2014-07-17
申请号：US14180248
申请日：2014-02-13
申请人： EDICO GENOME CORP.
发明人： Pieter Van Rooyen , Robert McMillen , Michael Ruehle
IPC分类号： G06F19/22
CPC分类号： G06F19/22 , G06F19/28
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

5. 发明公开

US20240170102A1 Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform 审中-公开
公开(公告)号：US20240170102A1
公开(公告)日：2024-05-23
申请号：US18414443
申请日：2024-01-16
申请人： Edico Genome, Corp.
发明人： Pieter van Rooyen , Michael Ruehle , Robert J. McMillen , Mark Hahm
IPC分类号： G16B50/00 , G16B30/00 , G16B30/10 , G16B40/00 , G16B40/30 , G16B50/30 , H03K19/17736
CPC分类号： G16B50/00 , G16B30/00 , G16B30/10 , G16B40/00 , G16B40/30 , G16B50/30 , H03K19/17736
摘要： A system, method and apparatus for executing an HMM analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the HMM analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the HMM analysis.

6. 发明授权

US10068183B1 Bioinformatics systems, apparatuses, and methods executed on a quantum processing platform 有权
公开(公告)号：US10068183B1
公开(公告)日：2018-09-04
申请号：US15497149
申请日：2017-04-25
申请人： Edico Genome, Corp.
发明人： Pieter van Rooyen
IPC分类号： G06N99/00 , G06F19/18 , G06N7/00 , G06K9/62 , G06F17/30 , G06F19/28 , G06F19/22
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes a quantum computing device formed of a set of hardwired quantum logic circuits interconnected by a plurality of superconducting connections to process information represented as a quantum state that is configured as a set of one or more qubits. The hardwired quantum logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired quantum logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired quantum logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

7. 发明授权

US10068054B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US10068054B2
公开(公告)日：2018-09-04
申请号：US15059221
申请日：2016-03-02
申请人： EDICO GENOME, CORP.
发明人： Pieter Van Rooyen , Michael Ruehle , Robert J. Mcmillen , Mark Hahm
IPC分类号： G06G7/50 , G06F19/24 , G06N3/00 , G06F19/22 , G06F19/28 , H03K19/177
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. In various instances, each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform one or more steps a variant call operation.

8. 发明授权

US09953134B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US09953134B2
公开(公告)日：2018-04-24
申请号：US15390303
申请日：2016-12-23
申请人： EDICO GENOME CORP.
发明人： Pieter van Rooyen , Robert J. McMillen , Michael Ruehle
IPC分类号： G06F19/00 , G06F19/28 , G06F19/22
CPC分类号： G06F19/28 , G06F13/16 , G06F13/4068 , G06F13/4265 , G06F19/22 , G06F19/24 , H01L21/768 , H01L21/76886 , H01L23/528 , H01L27/0207 , H01L27/118 , H01L27/11807 , H01L2027/11838 , H01L2027/11883 , H03K19/17736
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

9. 发明授权

US09652588B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US09652588B2
公开(公告)日：2017-05-16
申请号：US15376622
申请日：2016-12-12
申请人： Edico Genome Corp.
发明人： Pieter Van Rooyen , Robert J. Mcmillen , Michael Ruehle
IPC分类号： C40B60/10 , G06F19/22 , H01L21/768 , G06F19/24
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

10. 发明授权

US10083276B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US10083276B2
公开(公告)日：2018-09-25
申请号：US15144734
申请日：2016-05-02
申请人： Edico Genome Corporation
发明人： Pieter van Rooyen , Michael Ruehle , Robert J. Mcmillen
IPC分类号： G06F19/22 , H01L21/768 , H01L27/118 , G06F19/24 , G06F19/28 , H03K19/177 , H01L23/528 , H01L27/02
CPC分类号： G16B50/00 , G06F13/16 , G06F13/4068 , G06F13/4265 , G16B30/00 , G16B40/00 , H01L21/768 , H01L21/76886 , H01L23/528 , H01L27/0207 , H01L27/118 , H01L27/11807 , H01L2027/11838 , H01L2027/11883 , H03K19/17736
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

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