Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby

• US 8,380,442 B2
• Filed: 10/31/2007
• Issued: 02/19/2013
• Est. Priority Date: 06/26/2001
• Status: Expired due to Fees

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Ecker, David J., Griffey, Richard H., Sampath, Rangarajan, Hofstadler, Steven A., McNeil, John, Crooke, Stanley T.
• Primary Examiner(s): Clow, Lori A.
• Application Number:
  US11/930,108
• Publication Number:
  US 20110172925A1
• Time in Patent Office: 1,938 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/10 Nucleic acid folding
• 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 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 99/00 Subject matter not provided for in other groups of this subclass
• CPC Class Codes: G16H 50/80 for detecting, monitoring or modelling epidemics or pandemics, e.g. flu
• 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

The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.

Claims

1. A system, comprising:

a) a molecular mass determination component;

b) a database component stored on a computer readable medium comprising nucleic acid base compositions of amplification products from a plurality of bioagents each indexed to a primer pair and a bioagent wherein said amplification products comprise a variable sequence region 50-250 nucleobases in length flanked by conserved sequence regions 10 to 100 nucleobases in length wherein said primer pair hybridizes to said conserved regions, wherein said plurality of bioagents comprises bioagents from two or more different genera; and

c) a processor configured to convert molecular mass data to nucleic acid base composition data, wherein said processor is further configured to compare said base composition data from a bioagent to said database component comprising nucleic acid base compositions from a plurality of bioagents to identify said bioagent.

2. The system of claim 1, further comprising a nucleic acid purification component.

3. The system of claim 2, wherein said nucleic acid purification component comprises one or more buffer manipulations, one or more salt manipulations, one or more thermal manipulations, one or more pH manipulations, one or more mechanical manipulations, one or more centrifugation manipulations, or one or more magnetic manipulations.

4. The system of claim 1, further comprising a nucleic acid amplification component.

5. The system of claim 4, wherein said nucleic acid amplification component comprises a thermocycler.

6. The system of claim 4, wherein said nucleic acid amplification component further comprises one or more salts, one or more buffers, one or more purified oligonucleotide primers, one or more deoxynucleotide triphosphates (dNTPS), or one or more enzymes.

7. The system of claim 1, wherein said molecular mass determination component comprises a mass spectrometer.

8. The system of claim 7, wherein said mass spectrometer is an ESI mass spectrometer.

9. The system of claim 1, wherein said base composition identification component comprises a processor.

10. The system of claim 9, further comprising a computer program on a computer readable medium configured to direct said processor to coordinate the operation of said nucleic acid component, said base composition determination component, and said base composition identification component.

11. The system of claim 9, wherein said processor is configured to process mass spectrometry data to base composition data.

12. The system of claim 9, wherein said processor is configured to process base composition data to identify a bioagent.

13. The system of claim 1, wherein said database of base compositions comprises at least 10 base compositions.

14. The system of claim 1, wherein said database of base compositions comprises at least 20 base compositions.

15. The system of claim 1, wherein said database of base compositions comprises at least 30 base compositions.

16. The system of claim 1, wherein said database of base compositions comprises at least 40 base compositions.

17. The system of claim 1, wherein said database of base compositions comprises at least 50 base compositions.

18. The system of claim 1, wherein said database of base compositions comprises at least 60 base compositions.

19. The system of claim 1, wherein said database of base compositions comprises at least 70 base compositions.

20. The system of claim 1, wherein said database of base compositions comprises at least 80 base compositions.

21. The system of claim 1, wherein said database of base compositions comprises at least 90 base compositions.

22. The system of claim 1, wherein said database of base compositions comprises at least 100 base compositions.

23. The system of claim 1, wherein said database of base compositions comprises at least 500 base compositions.

24. The system of claim 1, wherein said database of base compositions comprises at least 1000 base compositions.

25. The system of claim 1, wherein said plurality of bioagents comprises bioagents that differ by genus, species, sub-species, strain, sub-type or nucleotide polymorphism.

26. The system of claim 1, wherein said plurality of bioagents comprises one or more viral bioagents, one or more bacterial bioagents, one or more fungal bioagents, one or more protozoal bioagents, one or more parasitic bioagents, one or more mammalian bioagents, or one or more human bioagents.