System for genetic surveillance and analysis

• US 10,181,010 B2
• Filed: 12/10/2014
• Issued: 01/15/2019
• Est. Priority Date: 04/26/2005
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Patel, Chirag, Fuernkranz, Hans, Greenstein, Michael
• Primary Examiner(s): Brusca, John S
• Application Number:
  US14/566,651
• Publication Number:
  US 20150213192A1
• Time in Patent Office: 1,497 Days
• Field of Search: None
• 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. A method of performing genetic surveillance, comprising:

performing genetic assay analysis of a sample obtained from an individual member of a population using a reader-analyzer instrument, said reader-analyzer instrument comprising an integrated sample and assay preparation apparatus configured to capture said sample, suspend said sample in solution, and process said sample;

generating sample genetic data based on said genetic assay analysis using said reader-analyzer instrument, said reader-analyzer configured to capture said sample genetic data using optical analysis of fluorescent signals;

capturing contextual information associated with said sample using said reader-analyzer instrument, said contextual information comprising spatial information and temporal information;

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

communicating targeting instructions over a network to said reader-analyzer instrument, said targeting instructions identifying at least one of a bacteria, virus, pathogen, and target sequence for targeting by the reader-analyzer instrument.

2. The method of claim 1 further comprising communicating said spatial information and temporal information associated with said sample genetic data to a laboratory response network.

3. The method of claim 1 further comprising using at least one portable reader-analyzer instrument to perform genetic assay analysis of said sample.

4. The method of claim 1 further comprising communicating said spatial information and temporal information associated with said sample genetic data from a first reader-analyzer instrument to a second reader-analyzer instrument.

5. The method of claim 1, further comprising performing sample preparation steps on said sample based on information received over said network, said sample preparation steps including manipulation of at least one assay.

6. The method of claim 1 and wherein said manipulation is performed based on information received over said network.

7. The method of claim 1 wherein comprising generating said sample data comprises collecting data that identifies a presence or an absence of at least one pathogenic organism.

8. The method of claim 7 wherein said collecting data step is performed by analyzing at least one target sequence related to the at least one pathogenic organism.

9. The method of claim 1 further comprising collecting demographic information from said individual member of a population.

10. The method of claim 9 wherein said demographic information is associated with said spatial information, said temporal information and said sample genetic data.

11. The method of claim 1 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.

12. The method of claim 1 wherein said sample obtaining step is performed by the user of said reader-analyzer instrument.

13. The method of claim 1, wherein the integrated sample and assay preparation module is a microfluidics card.

14. The method of claim 13, wherein the microfluidics card comprises of a reaction chamber and a sample inlet port.

15. The method of claim 13, wherein the microfluidics card is configured to provide for detection of a detection probe.

16. The method of claim 15, wherein the detection probe is suitable for detecting single nucleotide polymorphisms.

17. The method of claim 1, wherein the reader-analyzer instrument is configured to retrieve said spatial information based on at least one of a global positioning device or a geographic lookup table using an internet protocol address.