Assessment of reaction kinetics compatibility between polymerase chain reactions

• US 8,293,473 B2
• Filed: 04/04/2006
• Issued: 10/23/2012
• Est. Priority Date: 04/04/2006
• Status: Expired due to Fees

• Current Assignee: Labonnet Ltd.
• Original Assignee: Labonnet Ltd.
• Inventors: Ales, Tichopad, Tzachi, Bar
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Thomas, David
• Application Number:
  US12/294,392
• Publication Number:
  US 20090176232A1
• Time in Patent Office: 2,394 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/25 involving enzymes not classifiable in groups C12Q1/26 - C12Q1/66
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: G01N 2333/9015 Ligases (6)

Abstract

A method compares amplification reaction kinetics between two or more quantitative polymerase chain reactions (PCR). These methods enable quality control and/or quality assessment for quantification of nucleic acids by PCR. The method estimates plurality of parameters from each reaction and compares them simultaneously between reactions.

Claims

1. A method for the assessment of compatibility of an individual PCR with a defined reference of PCRs comprising the steps of:

a) amplifying by PCR a nucleic acid together with a signaling agent in an investigated sample;

b) obtaining a reference set by amplifying by PCR a plurality of samples with a reference nucleic acid sequence together with a signaling agent;

c) obtaining a time series of signals from every PCR by reading and storing at a plurality of time points at least one signal whose intensity is related to the quantity of the nucleic acid sequence formed in the PCR;

d) from the time series of signals of every PCR, deriving a plurality of parameters characterizing change of the signal accompanying the reaction progression;

e) simultaneously comparing by a single statistical test the parameters of the investigated PCR with the parameters of the PCRs of the reference set;

f) based on the probability obtained from the statistical test, drawing an inference on the geometry of the reaction kinetics of the investigated PCR with the reference set, wherein a parallel geometry indicates reaction kinetics compatible between the investigated PCR and the reference set; and

g) informing a user about one or more PCRs with non-parallel geometry if this is elicited in step f.

3. The method of claim 1, wherein at least one parameter is obtained I by smoothing the amplification signal readings with a suitable equation and obtaining values of the equation variables.

4. The method of claim 3, wherein at least one of the parameters describes the slope of the tangent to the smoothing curve at a defined point.

5. The method of claim 1, wherein one of the parameters is the maximal value or mean of plurality of maximal values of the amplification signal.

6. The method of claim 1, wherein at least one parameter is obtained by differentiation or partition of two or more consecutive amplification signal values.

7. The method of claim 1, wherein at least one parameter is the value of the first, second or generally n-derivative at a defined point of the amplification time series of signals.

2. A method for the assessment of compatibility of individual amplification of a nucleic acid sequence with a defined reference nucleic acid sequence comprising the steps of:

a) amplifying by PCR the nucleic acid together with a signaling agent in a sample;

b) obtaining a reference set by amplifying by PCR a plurality of samples with a reference nucleic acid sequence together with a signaling agent;

c) obtaining a time series of signals from every PCR by reading and storing at a plurality of time points at least one signal whose intensity is related to the quantity of the nucleic acid sequence formed in the PCR;

d) determining the signal in every PCR as a function of the amplification time, wherein the time can also be expressed as a number of reaction cycles;

e) calculating the first, second or generally the n-th order derivatives of said function, wherein n is an integer;

f) determining the ordinate maxima of at least two said derivatives as parameters for characterizing the reaction;

g) simultaneously comparing by a single statistical test the parameters of the investigated PCR with the parameters of the reference set, wherein a parallel geometry indicates reaction kinetics compatible between the investigated PCR and the reference set;

h) based on the probability obtained by the statistical test, drawing an inference on the geometry of the reaction kinetics of the investigated PCR with those of the PCRs of the reference set; and

i) informing a user about one or more PCRs with non-parallel geometry if this is elicited in step h.

8. A method for the assessment of compatibility between two or more groups of PCRs with an amplified nucleic acid sequence comprising the steps of:

a) amplifying by PCR the nucleic acid together with a signaling agent in samples assigned to two or more defined groups;

b) obtaining a time series of signals from every PCR by reading and storing at a plurality of time points at least one signal whose intensity is related to the quantity of the nucleic acid sequence formed in the PCR;

c) from the time series of signals of every PCR, deriving a plurality of at least two parameters characterizing change of the signal accompanying the reaction progression;

d) simultaneously comparing by a single statistical test the parameters between the groups of PCRs;

e) based on the probability obtained from the statistical test, drawing an inference on the geometry of the reaction kinetics of PCRs between the groups, wherein a parallel geometry indicates reaction kinetics compatible between the groups; and

f) informing a user about non-parallel geometry of PCRs between the groups if this is elicited in step e.

9. A method for the assessment of compatibility between two or more groups of samples with amplified nucleic acid sequence comprising the steps of:

a) amplifying by PCR the nucleic acid together with a signaling agent in samples assigned to two or more defined groups;

b) obtaining a time series of signals from every PCR by reading and storing at a plurality of time points at least one signal whose intensity is related to the quantity of the nucleic acid sequence formed in the PCR;

c) determining the signal in every PCR as a function of the amplification time, wherein the time can also be expressed as a number of reaction cycles;

d) calculating the first, second or generally the n-th order derivatives of said function, wherein n is an integer;

e) determining the ordinate maxima of at least two said derivatives as parameters for characterizing the reaction;

f) simultaneously comparing by a single statistical test the parameters between the groups of PCRs;

g) based on the probability obtained from the statistical test, drawing an inference on the geometry of the reaction kinetics of PCRs between the groups, wherein a parallel geometry indicates reaction kinetics compatible between the groups; and

h) informing a user about non-parallel geometry of PCRs between the groups if this is elicited in step g.

10. The method of claim 9, wherein at least one parameter is obtained by smoothing the amplification signal readings with a suitable equation and obtaining values of the equation variables.

11. The method of claim 10, wherein at least one of the parameters describes the slope of the tangent to the smoothing curve at a defined point.

12. The method of claim 11, wherein one of the parameters is the maximal value or mean of plurality of maximal values of the amplification signal.

13. The method of claim 11, wherein at least one parameter is obtained by differentiation or partition of two or more consecutive amplification signal values.

14. The method of claim 11, wherein at least one parameter is the value of the first, second or generally n-derivative at a defined point of the amplification time series of signals.