Healthcare analysis stream management

• US 9,953,137 B2
• Filed: 07/03/2013
• Issued: 04/24/2018
• 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:
  US13/935,371
• Publication Number:
  US 20140012843A1
• Time in Patent Office: 1,756 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, the annotations comprising alignment data between the sequence data and a pre-existing genome database;

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 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 100 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.

4. The system of claim 3, wherein X is 100 and Y is one day.

5. The system of claim 3, wherein X is 100 and Y is one hour.

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

7. The system of claim 1, wherein the sequencing device interface is configured to obtain the sequence data from at least 5 sequencing devices in parallel.

8. The system of claim 7, wherein the sequencing device interface is configured to obtain the sequence data from at least 10 sequencing devices in parallel.

9. The system of claim 1, wherein the genome data comprises genomic data of the patients individually.

10. The system of claim 1, wherein the analysis engine is configured to generate a notification as a function of the genome data.

11. The system of claim 10, wherein the notification comprises a request to obtain a higher confidence level with respect to the sequenced data.

12. The system of claim 10, wherein the notification configures a route within the analysis network.

13. The system of claim 1, wherein the analysis engine is configured to establish processing routes among the analysis nodes according to which at least one of the sequenced data and genome data is routed.

14. The system of claim 13, wherein the processing routes are established as a function of a priority.

15. The system of claim 1, wherein the analysis nodes are configured to exchange at least some of the sequence data and the genome data.

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

17. The system of claim 1, wherein the analysis nodes comprise high performance computing facilities.

18. The system of claim 17, wherein the analysis nodes comprise at least five high performance computing facilities.

19. The system of claim 1, wherein the analysis engine processes the sequence data to generate the genome data as a function of a normalized genomic sequence.

20. The system of claim 19, wherein the normalized genomic sequence comprises a statistical compilation from a population of patients.

21. The system of claim 19, wherein the genome data comprises at least one of the following with respect to the normalized genomic sequence:

a hot spot, a weighted reference point, and a prioritization for analysis.

22. The system of claim 1, further comprising a management interface configured to allow a user to provide feedback to the sequencing device via the sequencing device interface.

23. The system of claim 22, wherein the feedback includes sequencing device instructions.

24. The system of claim 23, wherein the sequencing device instructions include at least one of the following:

repeat sequencing target sequence area, halt sequencing, start sequencing, send data upon satisfaction of a trigger, delete sequence data from sequencing device, licensing management instructions, prioritizing sequence events, forwarding instructions of sequence data, and scheduling sequencing.

25. The system of claim 22, wherein the user comprises at least one of the following:

an analysis node, a healthcare provider, a researcher, a sequencing device manager, an analysis system manager, and a patient.

26. 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.

27. 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.

28. The system of claim 1, the annotations further comprising data identifying a putative or actual sequence location in a genome.

29. The system of claim 1, the annotations further comprising an order of analysis of genes.

30. A genomic analysis system comprising:

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

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 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.