Accurate identification of organisms based on individual information content

• US 8,527,207 B2
• Filed: 05/15/2008
• Issued: 09/03/2013
• Est. Priority Date: 05/15/2007
• Status: Expired due to Fees

• Current Assignee: ThinkVillage Corporation
• Original Assignee: ThinkVillage Corporation
• Inventors: Rogan, Peter K.
• Primary Examiner(s): Riggs, II, Larry D
• Application Number:
  US12/152,610
• Publication Number:
  US 20080286797A1
• Time in Patent Office: 1,937 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/701 Specific hybridization probes
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• 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 30/10 Sequence alignment; Homology search
• 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 40/30 Unsupervised data analysis

Abstract

An improved method for specific identification of any organisms by DNA hybridization or amplification is disclosed. Oligonucleotides are designed based on information analysis of sequences from a large number of related species. Oligonucleotide sequences that have the maximal specificity to certain nucleic acids from a particular species (or set of species) or type strain are selected for hybridization or amplification using DNA from the target organism. The presence or absence of a PCR or hybridization product may be used to identify the target organism. The resulting PCR products may also be compared with a DNA sequence database to obtain the identity of the organisms. The methods may prove useful in areas where rapid and accurate identification of an organism is desirable, such as in a hospital where identification of infectious agents may be critical, in the ethanol or beer industry where certain bacteria may be detrimental to the manufacturing process, or in the porcine industry where identification of different type strains of the porcine reproductive and respiratory syndrome virus (PRRV) is important for disease prevention.

Claims

1. A method for identification of an organism, comprising the steps of:

a) aligning a set of related sequences, wherein said set of related sequences comprise at least one polynucleotide sequence from said organism;

b) searching for a segment with low average information content from said set of aligned related sequences;

c) selecting from said segment one or more sequences with low individual information contents or a portion thereof as oligonucleotides for identification of said organism; and

d) hybridizing said oligonucleotides with at least one DNA molecule obtained from said organism,

wherein the average information content is determined by calculating and comparing the values of R_sequence for every equal-length window on said aligned sequences.

2. The method of claim 1, wherein the search for the segment with low average information content is by locating high and low average information content sequence windows along the entire length of said polynucleotide molecule.

3. The method of claim 2, wherein the length of the sequence window is in the range of 20-25 nucleotides.

4. The method of claim 1, wherein the polynucleotide molecule is a ribosomal DNA molecule.

5. The method of claim 1, wherein the organism is a porcine reproductive and respiratory syndrome virus.

6. The method of claim 1, wherein the organism is an organism which negatively affects the production of ethanol from a biomaterial.

7. The method of claim 1, wherein the organism is an organism which spoils the fermentation process of a beverage.

8. The method of claim 4, further comprising a step of using said oligonucleotide as a primer for amplifying at least one DNA molecule obtained from said organism by at least one reaction selected from polymerase chain reaction and ligase chain reaction.

9. A method for identification of an organism, comprising the steps of:

a) aligning a first polynucleotide sequence known to exist in a first organism with at least one additional related polynucleotide sequence from at least one different organism, said at least one additional related polynucleotide sequence being different from one another and from said first polynucleotide sequence;

b) searching for a window with low average information content on said aligned sequences;

c) selecting from said first polynucleotide sequence at least one segment with low individual information content or a portion thereof as an oligonucleotide for identification of said first organism; and

d) hybridizing said oligonucleotides with at least one DNA molecule obtained from said organism,

wherein the average information content is determined by calculating and comparing the values of R_sequence for every equal-length window on said aligned sequences.

10. The method of claim 9, wherein the selected segment has an R_i value that is at least one standard deviation below the average information content of sequences within the same window on the aligned polynucleotide sequences demarcated by the boundaries of the selected segment.

11. The method of claim 9, wherein said first organism and said at least one different organism are different type strains belonging to the same species.

12. The method of claim 9, wherein said first organism and said at least one different organism belong to different species.

13. The method of claim 9, wherein all polynucleotide sequences are DNA sequences.

14. The method of claim 13, further comprising a step of hybridizing said oligonucleotide with at least one DNA molecule obtained from said first organism.

15. The method of claim 13, further comprising a step of using said oligonucleotide as a primer for amplifying at least one DNA molecule obtained from said first organism by using a reaction selected from the group consisting of polymerase chain reaction and ligase chain reaction.

16. A method for identification of a type strain, comprising the steps of:

a) aligning a first polynucleotide sequence known to exist in a first type strain with at least one additional polynucleotide sequence from at least one different type strain, wherein said at least one additional polynucleotide sequence is different from one another and from said first polynucleotide sequence, and said first type strain and said at least one different type strain belong to the same species;

b) searching for a window with low average information content on said aligned sequences; and

c) selecting from said first polynucleotide sequence at least one segment with low individual information content or a portion thereof as an oligonucleotide for identification of said first type strain.

17. The method of claim 16, wherein said first type strain and said at least one different type strain are type strains of a porcine reproductive and respiratory syndrome virus.

19. The method of claim 16, further comprising a step of using said oligonucleotide as a primer for amplifying at least one DNA molecule obtained from said first strain by using a reaction selected from the group consisting of polymerase chain reaction and ligase chain reaction.

18. A method for identification of an organism, comprising the steps of:

a) aligning a first polynucleotide sequence known to exist in a first organism with at least one additional related polynucleotide sequence from at least one different organism, said at least one additional polynucleotide sequence being different from one another and from said first polynucleotide sequence;

b) searching for a window with low average information content on said aligned sequences, wherein the average information content is determined by calculating and comparing the values of R_sequence for every equal-length segment in the aligned sequences; and

c) selecting from said first polynucleotide sequence at least one segment with low individual information content or a portion thereof as an oligonucleotide for identification of said first organism.

20. The method of claim 18, further comprising a step of using said oligonucleotide as a primer for amplifying at least one DNA molecule obtained from said first organism by using a reaction selected from the group consisting of polymerase chain reaction and ligase chain reaction.