System for genetic surveillance and analysis

• US 20070026426A1
• Filed: 04/26/2006
• Published: 02/01/2007
• Est. Priority Date: 04/26/2005
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Patel, Chirag, Fuernkranz, Hans
• Application Number:
  US11/412,030
• Publication Number:
  US 20070026426A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 50/80 for detecting, monitoring or modelling epidemics or pandemics, e.g. flu
• CPC Class Codes: G16Z 99/00 Subject matter not provided for in other main groups of this subclass
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

A genetic surveillance system comprises a communications network and at least one reader-analyzer instrument. The reader-analyzer instrument has a communication interface to communicate over the network. The reader-analyzer instrument is adapted to perform genetic assay analysis of a sample obtained from a member of a population and to generate detection-related data based upon the analysis. The reader-analyzer instrument is adapted to associate qualifying information with the detection-related data and to communicate the associated qualifying information and detection-related data over the network.

Claims

1. An genetic surveillance information system, comprising:

a communications network;

at least one reader-analyzer instrument having communication interface to communicate over said network;

said reader-analyzer instrument being adapted to perform genetic assay analysis of a sample obtained from an individual member of a population and to generate genetic surveillance-related data based on said analysis;

said reader-analyzer instrument being adapted to associate spatial information and temporal information with said genetic surveillance-related data and to communicate said spatial information and temporal information associated with said genetic surveillance-related data over said network.

2. The system of claim 1 further comprising a database system communicating with said network and configured to store said spatial information and temporal information with associated said genetic surveillance-related data as information reflecting the status of said population.

3. A system to provide data to a laboratory response network according to claim 1 further comprising a software system that provides an interface between said laboratory response network and said network whereby said spatial information and temporal information with associated said genetic surveillance-related data is made available to said laboratory response network.

4. A system to provide data to a laboratory response network according to claim 2 further comprising a software system that provides an interface between said laboratory response network and said database whereby said spatial information and temporal information with associated said genetic surveillance-related data is made available to said laboratory response network.

5. The system of claim 1 wherein said reader-analyzer is a portable instrument.

6. The system of claim 1 wherein said reader-analyzer is adapted to process samples carried on a card having genetic assay materials carried thereon and adapted to be inserted into said reader-analyzer.

7. The system of claim 1 wherein said reader-analyzer instrument performs PCR analysis.

8. The system of claim 1 wherein said reader-analyzer instrument includes at least one hybridization array.

9. The system of claim 1 wherein said reader-analyzer instrument is adapted for bidirectional communication.

10. The system of claim 1 further comprising a plurality of said reader-analyzer instruments adapted for peer-to-peer communication with one another.

11. The system of claim 1 wherein said reader-analyzer instrument is adapted to receive control instructions via said network.

12. The system of claim 1 wherein said reader-analyzer instrument is adapted to alter the manner in which said genetic surveillance-related data are generated based on information received by said reader-analyzer over said network.

13. The system of claim 1 further comprising integrated sample preparation module to process said sample prior to analysis by said reader-analyzer instrument.

14. The system of claim 13 wherein said integrated sample preparation module has a communication interface to communicate over said network.

15. The system of claim 13 wherein said integrated sample preparation module is adapted to receive control instructions via said network.

16. The system of claim 13 wherein said integrated sample preparation module is adapted to alter the manner in which said sample is processed based on information received by said sample preparation module over said network.

17. The system of claim 13 wherein said integrated sample preparation module manipulates at least one assay.

18. The system of claim 13 wherein said integrated sample preparation module manipulates at least one assay, and wherein said integrated sample preparation module is adapted to alter the manner in which said assay manipulation is performed based on information received by said sample preparation module over said network.

19. The system of claim 1 further comprising data identifying a presence or absence of at least one pathogenic organism.

20. The system of claim 19 wherein said data is collected from analysis of at least one target sequence related to the at least one pathogenic organism.

21. The system of claim 1 further comprising obtaining demographic information from said individual member of a population.

22. The system of claim 21 wherein said demographic information is associated with said spatial information, said temporal information and said genetic surveillance-related data.

23. The system of claim 1 further comprising a database on electronic media operable for storing and analyzing said spatial information and temporal information with associated said genetic surveillance-related data retrieve from said network.

24. The system of claim 1 further comprising an algorithm for predicting potential danger to the population based on said spatial information and temporal information with associated said genetic surveillance-related data.

25. The system of claim 1 further comprising a learning algorithm for determining validity of new data based on lessons learn from said spatial information and temporal information with associated said genetic surveillance-related data.

26. A method of performing genetic surveillance, comprising:

using at least one reader-analyzer instrument to perform genetic assay analysis of a sample obtained from an individual member of a population and to generate genetic surveillance-related data based on said analysis;

associating spatial information and temporal information with said genetic surveillance-related data; and

communicating said spatial information and temporal information associated with said genetic surveillance-related data over a network using said reader-analyzer instrument to effect said communication.

27. The method of claim 26 further comprising storing said spatial information and temporal information with associated said genetic surveillance-related data in a database as information reflecting the status of said population.

28. The method of claim 26 further comprising communicating said spatial information and temporal information associated with said genetic surveillance-related data to a laboratory response network.

29. The method of claim 26 further comprising using at least one portable reader-analyzer instrument to perform genetic assay analysis of said sample.

30. The method of claim 26 further comprising communicating said spatial information and temporal information associated with said genetic surveillance-related data from a first reader-analyzer instrument to a second reader-analyzer instrument.

31. The method of claim 30 wherein said communication from a first reader-analyzer instrument to a second reader-analyzer instrument is effected peer-to-peer.

32. The method of claim 26 further comprising sending control instructions to said at least one reader-analyzer instrument via said network.

33. The method of claim 26 further comprising altering the manner in which said genetic surveillance-related data are generated based on information received by said reader-analyzer over said network.

34. The method of claim 26 further comprising performing sample preparation steps on said sample based on information received over said network.

35. The method of claim 34 wherein said sample preparation steps include manipulation of at least one assay.

36. The method of claim 34 wherein said sample preparation steps include manipulation of at least one assay and wherein said assay manipulation is performed based on information received over said network.

37. The method of claim 26 further comprising generating said surveillance-related data by collecting data identifying a presence or absence of at least one pathogenic organism.

38. The method of claim 27 wherein said collecting data step is performed by analyzing at least one target sequence related to the at least one pathogenic organism.

39. The method of claim 26 further comprising collecting demographic information from said individual member of a population.

40. The method of claim 39 wherein said demographic information is associated with said spatial information, said temporal information and said genetic surveillance-related data.

41. The method of claim 26 further comprising using said spatial information, said temporal information and said genetic surveillance-related data to predict potential danger to the population.

42. The method of claim 26 further comprising applying a learning algorithm to said spatial information, said temporal information and said genetic surveillance-related data to validate data acquired subsequent to said generation of surveillance-related data.

43. The method of claim 26 wherein said reader-analyzer instrument is associated with an automatic sensing device and the sample obtaining step is performed automatically by said automatic sensing device.

44. The method of claim 26 wherein said sample obtaining step is performed by the user of said reader-analyzer instrument.

45. A computer program product for enabling a networked computer system to perform genetic surveillance, comprising:

at least one computer readable medium bearing software instructions for enabling predetermined operations, the predetermined operations including;

using at least one reader-analyzer instrument to perform genetic assay analysis of a sample obtained from an individual member of a population and to generate genetic surveillance-related data based on said analysis;

associating spatial information and temporal information with said genetic surveillance-related data; and

communicating said spatial information and temporal information associated with said genetic surveillance-related data over a network using said reader-analyzer instrument to effect said communication.

46. The computer program product of claim 45 wherein at least one computer readable medium is associated with said reader-analyzer instrument.

47. The computer program product of claim 45 further comprising plural computer readable media bearing software instructions for enabling said predetermined operations, where said plural computer readable media are associated with plural reader-analyzer instruments.

48. The computer program product of claim 45 wherein said communicating said spatial information and temporal information associated with said genetic surveillance-related data over a network is effected peer-to-peer.

49. The computer program product of claim 45 wherein said software instructions further implement a learning algorithm that uses said spatial information, said temporal information and said genetic surveillance-related data to validate data acquired subsequent to said generation of surveillance-related data.