Healthcare analysis stream management

• US 10,095,835 B2
• Filed: 11/28/2016
• Issued: 10/09/2018
• Est. Priority Date: 07/06/2012
• Status: Active Grant

• Current Assignee: Nant Holdings IP, LLC (NantWorks, LLC)
• Original Assignee: Nant Holdings IP, LLC (NantWorks, LLC)
• Inventors: Soon-Shiong, Patrick
• Primary Examiner(s): NEGIN, RUSSELL SCOTT
• Application Number:
  US15/362,653
• Publication Number:
  US 20170076050A1
• Time in Patent Office: 680 Days
• Field of Search: None
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16H 10/60 for patient-specific data, e.g. for electronic patient records
• CPC Class Codes: G16H 30/20 for handling medical images, e.g. DICOM, HL7 or PACS
• CPC Class Codes: G16H 30/40 for processing medical images, e.g. editing
• CPC Class Codes: G16H 40/00 ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices
• CPC Class Codes: G16H 70/00 ICT specially adapted for the handling or processing of medical references
• CPC Class Codes: H04L 67/01 Protocols
• CPC Class Codes: H04L 67/02 based on web technology, e.g. hypertext transfer protocol [HTTP]
• CPC Class Codes: H04L 67/10 in which an application is distributed across nodes in the network software deployment G06F8/60; multiprogramming arrangements G06F9/46
• CPC Class Codes: H04L 67/12 specially adapted for proprietary or special-purpose networking environments, e.g. medical networks, sensor networks, networks in vehicles or remote metering networks
• CPC Class Codes: H04L 67/306 User profiles

Abstract

Apparatus, systems and methods for pre-processing, analyzing, and storing genomic data through a scalable, distributed analysis system across a network is presented.

Claims

1. A genomic analysis system comprising:

a plurality of sequencing devices configured to pre-process sequence data to generate pre-processed sequence data, the pre-processed sequence data comprising the sequence data and annotations;

a sequencing device interface configured to acquire pre-processed sequence data from the plurality of sequencing devices, where the sequence data is from a plurality of patients;

an analysis network; and

a plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to, based on the pre-processed sequence data, process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies.

2. The system of claim 1, wherein the analysis engine is configured to process sequence data from at least 10 patients in parallel.

3. The system of claim 1, wherein the analysis engine is configured to process sequence data into the genome data at a rate of at least X patients per Y unit of time, where X is at least 3 and Y is at most one day, and wherein X is ten and Y is one day.

4. The system of claim 1, wherein the analysis engine is configured to process sequence data into the genome data at a rate of at least X patients per Y unit of time, where X is at least 3 and Y is at most one day, and wherein X is ten and Y is one hour.

5. The system of claim 1, wherein the analysis network comprises an optic fiber data link.

6. The system of claim 5, wherein the analysis network comprises a continent spanning network.

7. The system of claim 1, wherein the sequencing device interface is configured to obtain the sequence data from at least 100 sequencing devices in parallel.

8. The system of claim 1, wherein the genome data comprises genomic data associated with a demographic of the patients.

9. The system of claim 1, wherein the analysis engine is configured to generate a notification as a function of the genome data, and wherein the notification comprises at least one of the following:

a processing status, an analysis engine management status, an alert, an alarm, a sequencing device instruction, an analysis recommendation, a prognosis, a diagnosis, and an inter-node communication.

10. The system of claim 1, wherein the analysis engine is configured to generate a notification as a function of the genome data, wherein the notification configures a route within the analysis network, and wherein the route allows the notification to be sent to at least one of the following:

a point-of-care, a sequencing device, a patient, and a healthcare service provider.

11. The system of claim 1, further comprising an engine management node configured to manage the analysis engine.

12. The system of claim 11, wherein the engine management node is configured to transmit an analysis status to a user.

13. The system of claim 11, wherein the engine management node is configured to generate an analysis dashboard.

14. The system of claim 1, wherein the analysis computer nodes comprise network switches.

15. The system of claim 1, wherein each of the analysis stream objects comprises an analysis data stream of the sequence data through processing to the genome data.

16. The system of claim 15, wherein the analysis data stream extends from a sequencing device through the sequencing device interface and through the analysis engine to an output device.

17. The system of claim 1, wherein the analysis stream object comprises at least one analysis route applied to the sequence data.

18. The system of claim 1, wherein the at least one stream management functionality comprises one of the following:

modifying an analysis route, instantiating an analysis stream according to the stream object, conducting a transaction based on the analysis stream object, altering an analysis, constructing notification trigger criteria based on the analysis stream object, and deconstructing an analysis stream.

19. The system of claim 1, wherein the sequencing device interface is configured to acquire sequence data through an image recognition algorithm applied to image data representing the sequence data, and wherein the image recognition algorithm operates as a function of a scale invariant feature transform.

20. The system of claim 1, wherein the sequencing device interface is configured to acquire sequence data through an image recognition algorithm applied to image data representing the sequence data, and wherein the sequencing device is further configured to translate the image data into a DNA base via serial time encoded amplified microscopy (STEAM).

21. The system of claim 1, wherein the analysis engine is configured to acquire sequence data through an image recognition algorithm applied to image data representing the sequence data, and wherein the image recognition algorithm operates as a function of a scale invariant feature transform.

22. The system of claim 1, wherein the analysis engine is configured to acquire sequence data through an image recognition algorithm applied to image data representing the sequence data, wherein the analysis engine is further configured to translate the image data into a DNA base via serial time encoded amplified microscopy (STEAM).

23. A genomic analysis system comprising:

a plurality of sequencing devices configured to pre-process sequence data to generate pre-processed sequence data, the pre-processed sequence data comprising the sequence data and annotations;

a sequencing device interface configured to acquire pre-processed sequence data from the plurality of sequencing devices, where the sequence data is from a plurality of patients;

an analysis network; and

a plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to, based on the pre-processed sequence data, process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies, wherein a first computer node of the plurality of analysis computer nodes and a second computer node of the plurality of analysis computer nodes are configured into a patient-specific analysis network topology, the first computer node of the plurality of analysis computer nodes applying a first analysis regime to the pre-processed sequence data, and the second computer node of the plurality of analysis computer nodes applying a second analysis regime to the pre-processed sequence data.

24. A genomic analysis system comprising:

a plurality of sequencing devices configured to pre-process sequence data to generate pre-processed sequence data, the pre-processed sequence data comprising the sequence data and annotations;

a sequencing device interface configured to acquire pre-processed sequence data from the plurality of sequencing devices, where the sequence data is from a plurality of patients;

an analysis network; and

a plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to, based on the pre-processed sequence data, process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies, wherein a first computer node of the plurality of analysis computer nodes and a second computer node of the plurality of analysis computer nodes are configured into a patient-specific analysis network topology, the first computer node of the plurality of analysis computer nodes operating on a first portion of the pre-processed sequence data, and the second computer node of the plurality of analysis computer nodes operating on a second portion of the pre-processed sequence data.

25. A genomic analysis system comprising:

a plurality of sequencing devices configured to pre-process sequence data to generate pre-processed sequence data, the pre-processed sequence data comprising the sequence data and annotations;

a sequencing device interface configured to acquire pre-processed sequence data from the plurality of sequencing devices, where the sequence data is from a plurality of patients;

an analysis network; and

a plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to, based on the pre-processed sequence data, process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies, wherein a first computer node of the plurality of analysis computer nodes and a second computer node of the plurality of analysis computer nodes are, based on an urgency indicated in the pre-processed sequence data, configured into a dedicated topology in analyzing the pre-processed sequence data of a single patient.

26. A genomic analysis system comprising:

a plurality of sequencing devices configured to pre-process sequence data to generate pre-processed sequence data, the pre-processed sequence data comprising the sequence data and annotations;

a sequencing device interface configured to acquire pre-processed sequence data from the plurality of sequencing devices, where the sequence data is from a plurality of patients;

an analysis network; and

a plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to, based on the pre-processed sequence data, process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies, wherein a first computer node of the plurality of analysis computer nodes is, based on an urgency indicated in the pre-processed sequence data, configured into a dedicated topology in analyzing the pre-processed sequence data of a single patient.

27. A genomic analysis system comprising:

a plurality of sequencing devices configured to pre-process sequence data to generate pre-processed sequence data, the pre-processed sequence data comprising the sequence data and annotations;

a sequencing device interface configured to acquire pre-processed sequence data from the plurality of sequencing devices, where the sequence data is from a plurality of patients;

an analysis network; and

a plurality of analysis computer nodes interconnected via the analysis network forming a genomic analysis engine having patient-specific analysis network topologies coupled with the sequencing device interface, and configured to, based on the pre-processed sequence data, process the sequence data from the patients in parallel into patient-specific genome data according to processing routes of the patient-specific analysis network topologies, wherein a first computer node of the plurality of analysis computer nodes is, based on an urgency indicated in the pre-processed sequence data, configured into a dedicated topology in analyzing the pre-processed sequence data.