System and method for nucleotide sequence profiling for sample identification

• US 8,101,353 B2
• Filed: 12/18/2008
• Issued: 01/24/2012
• Est. Priority Date: 12/18/2007
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Advanced Analytical Technologies, Inc. (Agilent Technologies, Inc.)
• Inventors: Procop, Gary W., Wei, Wei, Pang, Ho-ming
• Primary Examiner(s): Babic, Christopher M.
• Application Number:
  US12/338,373
• Publication Number:
  US 20100209908A1
• Time in Patent Office: 1,132 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2537/157 A reaction step characterised by the number of molecules incorporated or released

Abstract

The invention includes a method of sample profiling for identification. The method includes the steps of performing less than four nucleotide-specific chemical cleavage reactions to obtain nucleotide sequence fragments, performing size separation on the fragments, detecting the fragments'"'"' separation, generating a profile based on the detection, and comparing the profile to a data base to identify the sample.

Claims

1. A method of sample identification, comprising the steps of obtaining at least one nucleotide sequence template from the sample, amplifying the nucleotide sequence template, performing only three nucleotide-specific chemical cleavage reactions on the amplified template to obtain nucleotide sequence fragments, performing size-based separation on the nucleotide sequence fragments, detecting the fragments'"'"' separation, generating a unique profile based on the detection, and comparing the profile to a data base to identify the sample.

2. The method of claim 1, wherein the size-based separation includes an electrophoresis separation.

3. The method of claim 2, wherein the detecting the size separation step includes detecting a fluorescent dye label associated with the fragments.

4. The method of claim 1 wherein the detecting the size separation step includes detecting a fluorescent dye label associated with the fragments.

5. The method of claim 4, wherein the profile is an electropherogram.

6. The method of claim 2, wherein the detecting the size separation step includes detecting two different dye labels associated with the fragments.

7. The method of claim 1 wherein the detecting the size separation step includes detecting two different fluorescent dye labels associated with the fragments.

8. The method of claim 7, wherein the profile is an electropherogram.

9. The method of claim 1, wherein the profile is an electropherogram.

10. The method of claim 1, wherein the amplification step includes PCR.

11. The method of claim 1, wherein the nucleotide sequence is DNA.

12. The method of claim 1, wherein the sample is a microorganism.

13. The method of claim 1, wherein the sample is a gene.

14. A method of microorganism identification, comprising the steps of obtaining at least one nucleotide sequence template from the microorganism, amplifying the nucleotide sequence template, performing only three nucleotide-specific chemical cleavage reactions on the amplified template to obtain nucleotide sequence fragments, performing size-based separation on the nucleotide sequence fragments, detecting the fragments'"'"' separation, generating a profile based on the detection, and comparing the profile to a data base to identify the microorganism.

15. A method of microorganism identification, comprising the steps of obtaining at least one nucleotide sequence template from the microorganism, amplifying of the template with PCR on the template, performing only three nucleotide-specific chemical cleavage reactions on the amplified template to obtain nucleotide sequence fragments, performing size-based separation on the fragments with an electrophoresis separation, detecting the product fragments'"'"' separation by detecting a fluorescent dye label associated with the product, generating an electropherogram based on the detection, and comparing the electropherogram to a data base to identify the microorganism.