Methods and apparatus for genetic evaluation

• US 8,046,171 B2
• Filed: 04/18/2003
• Issued: 10/25/2011
• Est. Priority Date: 04/18/2003
• Status: Expired due to Fees

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories), Science Applications International Corporation
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Sofianos, Dino J., Stoughton, Roland B., Knize, Duane J., Murray, Dennis P., Lewis, Clifford T., Rudnick, Karl H., Robbins, David W., Larson, Brons M., Penhune, John P., Bar-on, Jonathan R., Basham, Cecil L. Jr., Hofstadler, Steven A., Sampath, Rangarajan, Griffey, Richard H., McNeil, John, Ecker, David J., Crooke, Stanley T.
• Primary Examiner(s): Clow; Lori A
• Application Number:
  US10/418,514
• Publication Number:
  US 20040209260A1
• Time in Patent Office: 3,112 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

Rapid and definitive bioagent detection and identification can be carried out without nucleic acid sequencing. Analysis of a variety of bioagents and samples, such as air, fluid, and body samples, can be carried out to provide information useful for industrial, medical, and environmental purposes. Nucleic acid samples of unknown or suspected bioagents may be collected, optimal primer pairs may be selected, and the nucleic acid may be amplified. Expected mass spectra signal models may be generated and selected, the actual mass spectra of the amplicons may be obtained. The expected mass spectra most closely correlating with the actual mass spectra may be determined using a joint maximum likelihood analysis, and base counts for the actual mass spectra and the expected mass spectra may be obtained. The most likely candidate bioagents may then be determined.

Claims

1. A system, comprising:

a) a mass spectrometer for obtaining a mass spectrum signal of a nucleic acid amplification product of an unknown bioagent, wherein said mass spectrum signal corresponds to a molecular mass of said nucleic acid amplification product, and wherein said nucleic acid amplification product is delineated by a primer set;

b) a signal processor for;

i) converting said mass spectrum signal to a base composition wherein said base composition identifies the number of, but not the nucleic acid gene sequence order of, A residues, C residues, T residues, and G residues in said amplification product,

ii) comparing said base composition of said nucleic acid amplification product of said unknown bioagent with a plurality of base compositions of virtual nucleic acid amplicons of known bioagents, wherein said virtual nucleic acid amplicons are delineated by said primer set, and wherein said base compositions of said virtual nucleic acid amplicons of known bioagents identify the number of, but not the nucleic acid gene sequence order of, A residues, C residues, T residues, and G residues in said virtual nucleic acid amplicons of known bioagents, and

iii) detecting a match of said base composition of said nucleic acid amplification product of said unknown bioagent with a base composition from said plurality of base compositions of virtual nucleic acid amplicons of known bioagents;

wherein said signal processor generates a report identifying said unknown bioagent based on said match.

2. The system of claim 1 wherein said signal processor estimates said one or more parameters and detects said match using a maximum likelihood detection algorithm.

3. The system of claim 2 wherein said maximum likelihood detection algorithm is configured to simultaneously consider a plurality of base compositions generated from virtual nucleic acid amplicons with a single primer pair.

4. The system of claim 2 wherein said maximum likelihood detection algorithm is configured to simultaneously consider a plurality of base compositions generated from virtual nucleic acid amplicons with a plurality of primer pairs.

5. The system of claim 4 wherein said plurality of primer pairs is five or more primer pairs.

6. The system of claim 1 further comprising a means for transferring one or more amplification products to said mass spectrometer.

7. The system of claim 1 further comprising a genomics database and a signal hypothesis predictor configured for transferring genomics data from said genomics database to said signal hypothesis predictor for prediction of said base compositions and transfer of said base compositions to said signal processor.

8. The system of claim 7 further comprising a signal model storage database configured for receiving said base composition from said signal hypothesis predictor, storing said base compositions and transferring said base compositions to said signal processor.

9. The system of claim 1 further comprising a noise estimator configured for processing noise from mass spectrometer data obtained from said mass spectrometer, producing a noise estimate and transferring said noise estimate to said signal processor and incorporated into said means for estimating said one or more parameters for said mass spectrum signal and detecting a match of said base composition with a base composition of said plurality of virtual nucleic acid amplicons.

10. The system of claim 1 wherein said signal processor comprises a generalized likelihood ratio test algorithm used to determine if a member of a list of pathogens is present in a sample comprising said amplification product.

11. The system of claim 1 wherein said signal processor comprises a mass deconvolution algorithm configured to identify unrecognized mass spectrum signals.

12. The system of claim 1 wherein said signal processor comprises a table of probabilities of detection of background organisms configured to identify probable background organisms in a sample comprising said nucleic acid amplification product.

13. The system of claim 1 wherein mass spectrum signal of said nucleic acid amplification product of said unknown bioagent comprises a real mass spectrum signal.

14. The system of claim 1 comprising a database of base counts corresponding to said plurality of virtual mass spectrum signals of virtual nucleic acid amplicons of known bioagents.

15. The system of claim 1 wherein said primer set comprises at least one primer pair that binds to nucleotide sequence regions that flank an intervening variable region.

16. The system of claim 15 wherein said nucleotide sequence regions comprise conserved regions.