Genomic informatics service

Patent metadata

Field	Value
Publication number	US-10528758-B2
Application number	US-201515307843-A
Country	US
Kind code	B2
Filing date	Apr 24, 2015
Priority date	May 2, 2014
Publication date	Jan 7, 2020
Grant date	Jan 7, 2020

Abstract

Methods and apparatus for a secure framework for storing and analyzing genomic data. Embodiments of the present invention apply persistent governance to sensitive information and to the analytics that operate upon it, managing the interaction between the two.

First claim

What is claimed is:

1. A method of securing genomic information, the method comprising:
receiving a genomic sequence from a source of genomic data;
generating a proxy patient identity for referencing the genomic sequence;
providing the genomic sequence to a managed computing pipeline, the computing pipeline being configured to process the genomic sequence so as to detect a feature in the genomic sequence;
annotating the detected feature, the detected feature and annotation together forming intermediate results;
storing the intermediate results in a data store;
obtaining the intermediate results from the managed computing pipeline at a hosted computing module comprising an isolated computing environment;
receiving, at an execution manager of the hosted computing module, a request to execute a user-specified program code configured to process the intermediate results to generate a set of informatics products;
decomposing, by the hosted computing module, the user-specified program code into individual computations within the isolated computing environment of the hosted computing module;
executing, by the hosted computing module, one or more requests from the user-specified program code for the stored intermediate results, wherein the stored intermediate results are provided to the isolated computing environment only if the user-specified program code is authorized to receive the stored intermediate results,
performing each computation using the isolated computing environment of the hosted computing module;
auditing the results of the user-specified program code computations; and
returning the results of the user-specified program code computations to a requester.

2. The method of claim 1 , wherein the genomic sequence is received from a sequencing apparatus.

3. The method of claim 1 further comprising storing at least one of the detected feature, the annotated feature, and the proxy identity in a database according to an auditable sequence of execution of the hosted computing module.

4. The method of claim 1 , wherein the hosted computing module is configured to annotate the detected feature according to a clinical relevance.

5. The method of claim 1 , further comprising aligning the genomic sequence against a reference genomic sequence prior to providing the genomic sequence to the managed computing pipeline.

6. The method of claim 1 , further comprising:
authenticating users using a security module of the hosted computing module; and
providing access control according to the user authentication.

7. The method of claim 1 , wherein in the step of providing the genomic sequence to the managed computing pipeline, the managed computing pipeline is secured by one of user authentication, and role-based access control.

8. The method of claim 1 , further comprising:
presenting at least one annotated feature and the associated patient proxy identity for clinical analysis.

9. An apparatus for providing genomic informatics, the apparatus comprising:
a receiver module configured to receive a genomic sequence from a source of genomic data;
a communication bus for providing the genomic sequence to a managed computing pipeline, the computing pipeline being configured to process the genomic sequence so as to detect a feature in the genomic sequence and annotate the detected feature, the detected feature and annotation together forming intermediate results, the intermediate results stored in a data store;
the communication bus being configured to obtain the intermediate results from the managed computing pipeline, and upon request to provide the intermediate results from the data store to a hosted computing module comprising an isolated computing environment; and
the hosted computing module being configured to receive at an execution manager, a request to execute a user-specified program code configured to process the stored intermediate results to generate a set of informatics products, wherein the hosted computing module is further configured to: (1) decompose the user-specified program code into individual computations within the isolated computing environment of the hosted computing module, (2) execute one or more requests from the user-specified program code for stored intermediate results, wherein the stored intermediate results are provided to the isolated computing environment only if the user-specified program code is authorized to receive the stored intermediate results, (3) perform each computation using the isolated computing environment of the hosted computing module; (4) audit the results of the user-specified program code computations; and (5) return the results of the user-specified program code computations to a requester.

10. The apparatus of claim 9 , wherein the source of genomic data is a sequencing apparatus.

11. The apparatus of claim 9 further comprising a non-transitory computer readable storage medium for storing at least one of the detected feature, the annotated feature, and the proxy identity in a database according to an auditable sequence of execution of the hosted computing module.

12. The apparatus of claim 9 wherein the hosted computing module is configured to annotate the detected feature according to a clinical relevance.

13. The apparatus of claim 9 further comprising a module configured to align the genomic sequence against a reference genomic sequence prior to providing the genomic sequence to the managed computing pipeline.

14. The apparatus of claim 9 wherein the hosted computing module comprises:
a program execution module comprising a virtualization container; and
a security module for authenticating users and providing access control according to the user authentication.

15. The apparatus of claim 9 wherein the managed computing pipeline is secured by one of user authentication and role-based access control.

16. The apparatus of claim 9 further comprising a user interface for presenting at least one annotated feature and the associated patient proxy identity for clinical analysis.

17. A method for performing a computation, the method comprising:
receiving a program for execution at a managed computing pipeline;
creating an execution context for the execution of the program;
launching a secure virtual machine within the execution context to execute the program;
receiving a genomic sequence and personally-identifiable information from a source of genomic data and annotating, by the program, a detected feature of the genome sequence to form intermediate results;
transmitting, upon request by the virtual machine, the intermediate results out of the managed computing pipeline to the virtual machine, wherein the intermediate results are provided to the virtual machine only if the program is authorized to receive the stored intermediate results;
executing the program within the virtual machine;
auditing the results of the executing program; and
returning the results of the executed program to a requester;
wherein the personally-identifiable information associated with the execution of the program is stored exclusively within the execution context.

18. The method of claim 17 further comprising creating an executable image from the uploaded program and saving the executable image to a non-transitory computer readable storage medium.

19. The method of claim 18 further comprising storing state information associated with the execution of the virtual machine in the non-transitory computer readable storage medium.

20. The method of claim 17 wherein the execut

Assignees

• Koninklijke Philips Nv
• Intertrust Tech Corp

Inventors

• Dimitrova Nevenka
• Carey William Knox
• Krasinski Raymond J
• Nilsson Jarl
• Grantham Bart
• Mankovich Alexander Ryan
• Agrawal Vartika

Classifications

• G16B50/00

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title

• G06F21/32

  using biometric data, e.g. fingerprints, iris scans or voiceprints · CPC title

• G16H10/60 Primary

  for patient-specific data, e.g. for electronic patient records · CPC title

• G06F21/6245 Primary

  Protecting personal data, e.g. for financial or medical purposes · CPC title

• G16B50/30

  Data warehousing; Computing architectures · CPC title