Real-time gene quantification with internal standards

• US 7,630,837 B2
• Filed: 08/29/2002
• Issued: 12/08/2009
• Est. Priority Date: 08/31/2001
• Status: Active Grant

• Current Assignee: Biofire Defense, University of Utah Research Foundation (State of Utah)
• Original Assignee: Idaho Technology, University of Utah Research Foundation (State of Utah)
• Inventors: Eyre, David J., Stevenson, Wade R., Caplin, Brian E., deSilva, Deepika Marine, Rasmussen, Randy P.
• Primary Examiner(s): Zhou; Shubo (Joe)
• Application Number:
  US10/230,489
• Publication Number:
  US 20030104438A1
• Time in Patent Office: 2,658 Days
• Field of Search: 435/91.2, 702/20
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2545/107 with a competitive internal standard/control
• CPC Class Codes: C12Q 2561/113 Real time assay
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels

Abstract

The present invention is directed to a nucleic acid quantification kit and method for determining the initial concentration or mass fraction of a target nucleic acid present in a sample. Illustrative embodiments include real-time competitive quantitative polymerase chain reaction (PCR) to determine the copy number or mass fraction of a target nucleic acid sequence in a sample and use of a thermodynamically based signal processing algorithm, with or without PCR, to provide mass fraction information.

Claims

1. A method of determining mass fractions of first and second target nucleic acids present in a test sample comprising:

obtaining an approximated standard melting signal, f_i, for each of the first and second target nucleic acids, the approximated standard melting signal for the first target nucleic acid corresponding to a change in fluorescence of the first target nucleic acid over temperature and the approximated standard melting signal for the second target nucleic acid corresponding to a change in fluorescence of the second target nucleic acid over temperature,

contacting the target nucleic acids in the test sample with a fluorescent nucleic acid indicator, the indicator being configured to provide a signal related to the quantity of indicator hybridized to the target nucleic acids, the indicator further configured to discriminate the target nucleic acids based on melting temperature,

illuminating the test sample including the fluorescent nucleic acid indicator,

cycling the illuminated test sample through an annealing temperature and a denaturing temperature that is higher than the annealing temperature,

monitoring fluorescent change of the illuminated test sample while changing temperature of the illuminated test sample to obtain a fluorescence melting signal, f_mix, of the test sample, the fluorescence melting signal, f_mix, corresponding to a change in fluorescence of the test sample over temperature, and

approximating the fluorescence melting signal, f_mix, for the test sample over temperature, T, as a combination of the approximated standard melting signals, f_i, of the first and second target nucleic acids, and using f_i and f_mix to determine the mass fractions, m_i, of the first and second target nucleic acids in the test sample according to the formula

${\int <br><br>}_{T_0}^{T_1}<br><br><br><br>f_{\mathrm{mix}}-\underset{i}{\sum <br><br>}<br><br><br><br>m_i<br><br>f_i(<br><br>T)<br><br><br><br>d<br><br>T.$

2. The method of claim 1 wherein the step of cycling the illuminated test sample through an annealing temperature and a denaturing temperature comprises:

raising the temperature of the illuminated test sample from the annealing temperature to the denaturing temperature,

holding the illuminated test sample at the denaturing temperature for a predetermined amount of time,

lowering the temperature of the illuminated test sample from the denaturing temperature to a temperature that is at least as low as the annealing temperature, and

holding the illuminated test sample at the temperature that is at least as low as the annealing temperature for at least a predetermined length of time.

3. The method of claim 2 wherein the step of cycling the illuminated test sample through an annealing temperature and a denaturing temperature further comprises thermocycling the illuminated test sample by executing the raising, lowering and both holding steps a predetermined number of times.

4. The method of claim 1 wherein the step of cycling the illuminated test sample through an annealing temperature and a denaturing temperature further comprises cycling the illuminated test sample through the annealing and denaturing temperatures for a predetermined number of repetitions.

5. The method of claim 1 wherein the step of cycling the illuminated test sample through an annealing temperature and a denaturing temperature further comprises cycling the illuminated test sample through the annealing temperature, the denaturing temperature and an elongation temperature for a predetermined number of repetitions.

6. The method of claim 1 wherein the step of monitoring fluorescent change comprises monitoring fluorescent change of the illuminated test sample once during each cycling of the illuminated test sample through the annealing temperature and the denaturing temperature.

7. The method of claim 1 wherein the step of monitoring fluorescent change comprises monitoring fluorescent change of the illuminated test sample continuously during cycling of the illuminated test sample through the annealing temperature and the denaturing temperature.

8. The method of claim 1 further comprising

approximating a fluorescence melting signal of a PCR reaction for each additional species that does not have an approximated standard melting signal, and

iteratively processing each of the approximated fluorescence melting signals to determine approximate standard melting signals to determine mass fractions of the additional species that do not have approximated standard melting signals according to a fit coupled thermodynamic and signal processing model.

9. The method of claim 8 wherein the iteratively processing step comprises:

solving the fit coupled thermodynamic and signal processing model using each of the approximated fluorescence melting signals and the approximate standard melting signals to obtain a solution,

determining whether the solution to the fit coupled thermodynamic and signal processing model is minimized, and

defining another approximated standard melting signal based on the solution and re-executing the solving step if the solution to the fit coupled thermodynamic and signal processing model is not minimized.

10. The method of claim 9 wherein the step of determining whether the solution to the fit coupled thermodynamic and signal processing model is minimized includes:

computing a sum of the mass fractions of the first and second target nucleic acids,

comparing the sum of the mass fractions to a difference 1-ε

, where ε

is a tolerance value, and

determining that the solution to the fit coupled thermodynamic and signal processing model is minimized if the sum of the mass fractions is greater than 1-ε

.

11. The method of claim 9 wherein the fit coupled thermodynamic and signal processing model is defined by

${\int \; <li></li>}_{T_0}^{T_1}<br><br><br><br>f_{\mathrm{mix}}^{\mathrm{\sigma <br><br>}}-\underset{i}{\sum <br><br>}<br><br>m_i<br><br>f_i^{\mathrm{\sigma <br><br>}}<br><br>\left(T\right)-f^r<br><br>\left(T\right)<br><br><br><br><br><br>d<br><br>T,$

wherein σ

is a smoothing parameter, f^σ

_mix represents each of the number of fluorescence melting signals that do not have approximated standard melting signals and that are greater than σ

, m_i is the mass fraction of each of the first and second target nucleic acids, f^σ

_i represents the approximated standard melting signals, and f^r (T) represents the approximated fluorescence melting signals.

12. The method of claim 1 wherein the mass fractions of the first and second target nucleic acids provides information concerning a deletion or duplication in a gene.

13. The method of claim 1 wherein the fluorescent nucleic acid indicator comprises a fluorescently-labeled sequence specific oligonucleotide probe.

14. The method of claim 13 wherein the sequence specific oligonucleotide probe is selected from the group consisting of a fluorescence resonance energy transfer pair probe system and a single-labeled oligonucleotide.

15. The method of claim 1 wherein the second target nucleic acid is a competitor of the first target nucleic acid for the fluorescent nucleic acid indicator.

16. The method of claim 1 wherein the test sample further comprises a thermostable polymerase and a pair of oligonucleotide primers configured to amplify the first target nucleic acid.