Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
A system, method and apparatus for executing a bioinformatics 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 bioinformatics 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 bioinformatics analysis.
1. A system for performing a bioinformatics analysis on genomic data from a subject using genetic reference sequence data, where each of the genomic data and the genetic reference sequence data represent a sequence of nucleotides, the system comprising:
a cloud computing cluster having one or more servers;
a memory associated with the one or more servers for storing the genomic data and the genetic reference sequence data; and
a field programmable gate array (FPGA) housed in at least one of the one or more servers, the FPGA comprising a set of hardwired digital logic circuits, the hardwired digital logic circuits being interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising a memory interface to access the memory, the hardwired digital logic circuits being 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 bioinformatics analysis on the genomic data, the set of processing engines comprising a first wired configuration to access the genomic data of the subject and the genetic reference sequence data, compare the sequence of nucleotides in the genomic data to the sequence of nucleotides of the genetic reference sequence data to determine one or more similarities or differences between the sequence of nucleotides in the genomic data and the sequence of nucleotides in the genetic reference sequence data to produce results data, the results data being storable in the memory; and
the cloud computing cluster being configured to access the memory, retrieve, and process the results data to generate one or more diagnostic, prophylactic and/or therapeutic evaluations based on the one or more similarities or differences.
2. The system according to claim 1 , further comprising a database connected with the cloud computing cluster for receiving and storing one or more electronic health records of the subject.
3. The system according to claim 2 ,
wherein the system further comprises a computing system that executes one or more third party applications,
wherein the computing system is further configured to access the one or more electronic health records of the subject from the database to compare the results data to one or more electronic health records of the subject, and to perform a tertiary analysis on the result data.
4. The system according to claim 3 , wherein the tertiary analysis comprises a diagnostic evaluation analysis.
5. The system according to claim 4 , wherein the bioinformatics analyses comprises a cancer evaluation analysis.
6. The system according to claim 4 , wherein the tertiary analysis is configured to predict a potential of an occurrence of a diseased state.
7. The system according to claim 6 , wherein the diseased state comprises cancer.
8. A system for executing a portion of a bioinformatics analysis pipeline on genomic data from a subject using genetic reference sequence data, where each of the genomic data and the genetic reference sequence data represent a sequence of nucleotides, the system comprising:
a cloud computing cluster having a plurality of servers;
a memory associated with the plurality of servers for storing the genomic data and the genetic reference sequence data; and
a bioinformatics analysis pipeline platform housed in one or more of the plurality of servers, the bioinformatics analysis pipeline platform comprising a data analysis module having a memory interface to access the genomic data of the subject and the genetic reference sequence data from the memory, the data analysis module having an FPGA configured to perform one or more steps in comparing the sequence of nucleotides in the genomic data to the sequence of nucleotides of the genetic reference sequence data, and to determine one or more similarities or differences between the sequence of nucleotides in the genomic data and the sequence of nucleotides in the genetic reference sequence data to produce results data, the results data being storage in the memory; and
the cloud computing cluster being configured to access the memory, retrieve and process the results data to generate one or more diagnostic, prophylactic and/or therapeutic evaluations representing the one or more similarities or differences.
9. The system according to claim 8 , further comprising a database connected with the cloud computing cluster for receiving one or more electronic health records of the subject.
10. The system according to claim 9 ,
wherein the system further comprises a computing system that executes one or more third party applications,
wherein the computing system is further configured to access the one or more electronic health records from the database to, compare the results data to the one or more electronic health records of the subject, and to perform a tertiary analysis on the result data.
11. The system according to claim 10 , wherein the tertiary analysis comprises a diagnostic evaluation analysis.
12. The system according to claim 11 , wherein the diagnostic analyses comprise a cancer evaluation analysis.
13. The system according to claim 10 , wherein the tertiary analysis is configured to predict a potential of an occurrence of a diseased state.
14. The system according to claim 13 , wherein the diseased state comprises cancer.
15. A genomics processing system for executing a portion of a genetic sequence analysis pipeline, the system comprising:
a cloud computing cluster having one or more servers, the cloud computing cluster having a memory associated with the one or more servers for storing a plurality of reads of genomic data of a subject and genetic reference sequence data, each read of genomic data and the genetic reference sequence data representing a sequence of nucleotides;
a computing system that executes one or more third party applications for executing the portion of the genetic sequence analysis pipeline using the plurality of reads of genomic data of the subject and the genetic reference sequence data stored in the memory; and
a sequence analysis pipeline platform connected with the memory and the computing system via one or more application programming interfaces (APIs), the sequence analysis pipeline platform comprising a diagnostic evaluations module to access, in response to the one or more third party applications executed by the computing system, the genomic data of the subject and the genetic reference sequence data from the memory, the diagnostic evaluations module having an FPGA configured for comparing the sequence of nucleotides in the genomic data of the subject to the sequence of nucleotides of the genetic reference sequence data, to determine one or more differences between the sequence of nucleotides in the genomic data of the subject and the sequence of nucleotides in the genetic reference sequence data, and the diagnostic evaluations module further being configured to generate one or more diagnostic evaluations representing the one or more similarities or differences.
16. The system according to claim 15 , further comprising a database connected with the cloud computing cluster for receiving one or more electronic health records of the subject.
17. The system according to claim 16 , wherein the computing system is further configured to access the one or more electronic health records from the database, compare the results data to one or more electronic health records of the subject, and to perform a tertiary analysis on the result data.
18. The system according to claim 17 , wherein the tertiary analysis comprises one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis.
19. The system according to claim 18 , wherein the one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis comprises a cancer evaluation analysis.
20. The system according to claim 18 , wherein the tertiary analysis is configured to predict a potential of an occurrence of a diseased state.
21. The system according to claim 20 , wherein the diseased state comprises cancer.
22. The system according to claim 21 , wherein the computing system is accessed by the one or more third party applications via at least one of the one or more APIs.
23. A cancer diagnostic system for performing a cancer diagnostic analysis on genomic data using genetic reference sequence data from a subject, where each of the genomic data and the genetic reference sequence data represent a sequence of nucleotides, the system comprising:
a cloud computing cluster having one or more servers;
a memory associated with the one or more servers for storing the genomic data and the genetic reference sequence data; and
a field programmable gate array (FPGA) housed in at least one of the one or more servers, the FPGA comprising a set of hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising a memory interface to access the memory, the hardwired digital logic circuits being 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 cancer diagnostic analysis on the genomic data, the set of processing engines comprising a first wired configuration to access the genomic data and the genetic reference sequence data, compare the sequence of nucleotides in the genomic data to the sequence of nucleotides of the genetic reference sequence data to produce results data, the results data comprising one or more similarities or differences between the sequence of nucleotides in the genomic data and the sequence of nucleotides in the genetic reference sequence data, the results data being storable in the memory; and the cloud computing cluster being configured to access the memory, retrieve, and process the results data to generate one or more diagnostic evaluations based on the one or more similarities or differences, the one or more diagnostic evaluations including an identification or likelihood of cancer.
24. The cancer diagnostic system according to claim 23 , further comprising a database connected with the cloud computing cluster for receiving one or more electronic health records of the subject.
25. The cancer diagnostic system according to claim 24 , wherein the cloud computing cluster is further configured to access the one or more electronic health records from the database, compare the results data to one or more electronic health records of the subject, and to perform a tertiary analysis on the result data.
26. The cancer diagnostic system according to claim 25 , wherein the tertiary analysis comprises one or more of diagnostic, prophylactic and/or therapeutic evaluation analysis.
27. The cancer diagnostic system according to claim 23 , further comprising one or more application programming interfaces (APIs) that provide accessibility to the cloud computing cluster by one or more third party applications via a communications network.
28. The cancer diagnostic system according to claim 27 , wherein the communications network is the Internet.