Cohort selection with privacy protection

• US 10,162,880 B1
• Filed: 07/01/2016
• Issued: 12/25/2018
• Est. Priority Date: 10/11/2011
• Status: Active Grant

• Current Assignee: 23andme Incorporated (23andMe Holding Co.)
• Original Assignee: 23andme Incorporated (23andMe Holding Co.)
• Inventors: Chowdry, Arnab, Kompel, Alexander, Polcari, Michael
• Primary Examiner(s): Hasan, Syed H
• Application Number:
  US15/201,257
• Time in Patent Office: 907 Days
• CPC Class Codes: G06F 16/2455 Query execution
• CPC Class Codes: G06F 16/285 Clustering or classification
• CPC Class Codes: G06F 16/86 Mapping to a database
• CPC Class Codes: G06F 16/9535 Search customisation based on user profiles and personalisation
• 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 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16H 10/60 for patient-specific data, e.g. for electronic patient records

Abstract

Assembling a cohort includes: receiving genetic characteristic information pertaining to a desired genetic characteristic; using the genetic characteristic information to search a data storage comprising information of previously genotyped individuals to derive a candidate group having the desired genetic characteristic; and assembling the cohort based at least in part on the candidate group.

Claims

1. A system, comprising:

one or more processors configured to;

(a) receive genetic characteristic information and/or phenotypic characteristic information pertaining to a desired genetic characteristic and/or phenotypic characteristic;

(b) using the genetic characteristic information and/or phenotypic characteristic information, search one or more data stores comprising genetic information and/or phenotypic information of individuals for whom genetic information and phenotypic information have been previously obtained to identify a candidate group comprising a plurality of individuals having the desired genetic characteristic and/or the phenotypic characteristic, wherein the one or more data stores further comprise contact information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores;

(c) assemble a cohort of one or more individuals based at least in part on the desired genetic characteristic and/or phenotypic characteristic of the plurality of individuals of the candidate group;

(d) in response to a request by a first user, having a first assigned role permitting access to genetic information and/or phenotypic information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores, to gain access to the genetic information and/or phenotypic information of the one or more individuals of the cohort, send at least some data pertaining to the genetic information and/or phenotypic information in the one or more data stores for the one or more individuals of the cohort assembled in (c), and prevent, pursuant to the first assigned role, the first user from accessing data pertaining to contact information of the one or more individuals of the cohort assembled in (c); and

(e) in response to a request by a second user, having a second assigned role permitting access to contact information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores, to gain access to contact information of the one or more individuals of the cohort assembled in (c), send data pertaining to the contact information of the one or more individuals of the cohort and prevent, pursuant to the second assigned role, the second user from accessing data pertaining to the genetic information and/or phenotypic information in the one or more data stores of the one or more individuals of the cohort assembled in (c); and

one or more memories coupled to the one or more processors, configured to provide the one or more processors with instructions and/or data.

2. The system of claim 1, wherein the one or more data stores comprise the genetic information of more than 100,000 individuals.

3. The system of claim 1, wherein the contact information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores is anonymized.

4. The system of claim 1, wherein the contact information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored comprises information selected from the group consisting of a name, street address, email address, internet account, phone number, and any combination thereof.

5. The system of claim 1, wherein the one or more processors are configured to prevent, pursuant to the first assigned role, the first user from finding out a real name of the one or more individuals of the cohort.

6. The system of claim 1, wherein at least one of the one or more data stores is configured to provide access control and thereby prevent a user with a particular assigned role from accessing unauthorized information of individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores.

7. The system of claim 6, wherein at least one of the one or more data stores is configured with one or more separate databases and/or separate tables to implement said access control.

8. The system of claim 1, wherein at least one of the one or more data stores further comprises a unique account identification that uniquely links each of the individuals for whom genetic information and phenotypic information have been previously obtained, and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores, to his/her contact information.

9. The system of claim 1, wherein the first assigned role permits access to the genetic information and/or phenotypic information of one or more individuals of the cohort for only a defined set of projects.

10. The system of claim 1, wherein the one or more processors are further configured to search the one or more data stores by:

identifying a personal identifier associated with each of the one or more individuals of the cohort assembled in (c);

looking up an account identifier associated with each of the one or more individuals of the cohort assembled in (c) in a mapping data store; and

sending account information for each of the one or more individuals of the cohort to the second user.

11. The system of claim 1, wherein the one or more processors are further configured to return results to a query only when at least a threshold number of the individuals for whom genetic information and phenotypic information have been previously obtained, and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores, is included in the results.

12. The system of claim 1, wherein the one or more processors are configured to:

receive genetic characteristic information and phenotypic characteristic information pertaining to the desired genetic characteristic and the desired phenotypic characteristic in (a), respectively; and

search the one or more data stores to identify the candidate group comprising the plurality of individuals having the genetic characteristic information and the phenotypic characteristic information in (b).

13. The system of claim 1, wherein the phenotypic characteristic information comprises health-related information.

14. The system of claim 1, wherein the phenotypic characteristic information comprises a disease condition, blood test result, liver panel test result, sex, and/or age.

15. The system of claim 1, wherein the genetic characteristic information comprises genetic information related to a health condition.

16. The system of claim 1, wherein the one or more data stores comprises a first data store comprising the genetic information and/or phenotypic information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores, and a second data store comprising the contact information of each of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores, wherein the first data store does not contain contact information of any individual and the second data store does not contain the genetic information and/or phenotypic information of any individual.

17. The system of claim 1, wherein each individual of the plurality of individuals of the candidate group is provided a survey to identify additional information not already included in the one or more data stores, and each individual of the plurality of individuals of the candidate group is identified at least in part based on results of the survey, and wherein the one or more processors are further configured to return results to the survey.

18. The system of claim 1, wherein the genetic information comprises genotypic information.

19. The system of claim 1, wherein the one or more data stores comprises a first database comprising the genetic information of individuals for whom genetic information has been previously obtained and a second database comprising the phenotypic information of individuals for whom phenotypic information has been previously obtained.

20. The system of claim 19, wherein a first data store of the one or more data stores includes the first database and the second database.

21. The system of claim 19, wherein a first data store of the one or more data stores includes the first database comprising the genetic information of individuals for whom genetic information has been previously obtained and a second data store of the one or more data stores includes the second database comprising the phenotypic information of individuals for whom phenotypic information has been previously obtained.

22. The system of claim 21, wherein the first data store and the second data store are on separate physical devices.

23. The system of claim 21, wherein the first data store and the second data store are on the same physical device.

24. The system of claim 1, wherein the one or more data stores comprises a first database comprising the genetic information and the phenotypic information of individuals for whom genetic information and phenotypic information has been previously obtained.

25. The system of claim 1, wherein at least one of the one or more data stores further comprises family history information pertaining to at least one of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores.

26. The system of claim 1, wherein at least one of the one or more data stores further comprises environmental information pertaining to at least one of the individuals for whom genetic information and phenotypic information have been previously obtained and for whom the genetic information and/or phenotypic information is/are stored in the one or more data stores.

27. The system of claim 1, wherein the one or more data stores includes genetic information of individuals for whom genetic information and phenotypic information have been previously obtained.

28. The system of claim 1, wherein the one or more data stores includes phenotypic information of individuals for whom genetic information and phenotypic information have been previously obtained.

29. The system of claim 1, wherein the one or more data stores includes genetic information and phenotypic information of individuals for whom genetic information and phenotypic information have been previously obtained.

30. The system of claim 28, wherein the genetic information and phenotypic information are in separate databases.