Method and system for analyzing reactions using an information system
A method and system for determining the quantity of an analyte initially present in a chemical and or biological reaction as well as a computer implemented method and system to automate portions of the analysis comprising mathematical or graphical analysis of an amplification reaction.
1. A method of determining whether a test sample contains a target nucleic acid, the method comprising:
(a) contacting the test sample with at least one amplification agent for an amplification reaction;
(b) measuring signals obtained at various points in the amplification reaction, the signals being proportional to the amount of the target nucleic acid present;
(c) determining an efficiency related transform of the amplification reaction;
(d) determining an efficiency related value that is the maximum magnitude of the efficiency related transform; and
(e) determining that the test sample contains a target nucleic acid if the efficiency related value for the amplification reaction exceeds a criterion value wherein, the criterion value is determined by (1) amplifying a plurality of samples to determine the efficiency related values and (2) selecting a value that separates the efficiency related values of negative samples from the efficiency related values of positive samples.
2. The method of claim 1 , wherein the efficiency related transform of the amplification reaction is selected from the group consisting of (1) ratio transform of the signals obtained from the amplification, (2) the derivative of the log of the signals obtained from the amplification, and (3) the first derivative of the signals obtained from the amplification.
3. The method of claim 2 , wherein the efficiency related transform is the first derivative of the signals obtained from the amplification, wherein the first derivative of the signals obtained from the amplification reaction is equal to the difference between two consecutive signals obtained from the amplification reaction divided by the magnitude of the interval between the consecutive signals.
4. The method of claim 2 , wherein the efficiency related transform is the first derivative of the signals obtained from the amplification, wherein the first derivative of the signals obtained from the amplification reaction is calculated by mathematical manipulation of a curve fitted to the signals obtained from the amplification reaction.
5. The method of claim 1 , wherein the step of determining whether the efficiency related value exceeds a criterion value is performed by comparing the efficiency related value to a criterion curve, wherein the criterion curve is determined by:
(a) performing a plurality of amplification reactions on negative samples, said negative samples being samples that lack the target nucleic acid;
(b) determining the efficiency related value for each negative sample;
(c) determining the mean and the standard deviation of the efficiency related values of the negative samples; and
(d) determining that any sample having any efficiency related value exceeding the mean by a selected multiple of the standard deviation of the efficiency related values of the negative samples contains the target nucleic acid.
6. The method of claim 5 , wherein any sample having any efficiency related value exceeding the mean by from one to about 20 times the standard deviation of the efficiency related transform of the negative samples is deemed to contain a target nucleic acid.
7. The method of claim 1 , wherein the efficiency related value occurs at a particular reaction point and the selected value of step (e) varies according to the particular reaction point at which the efficiency related value occurs.
8. The method of claim 1 , wherein the criterion value of step (e) is determined by (1) amplifying a plurality of samples to determine the efficiency related values and (2) selecting a value that is higher than all of the efficiency related values for negative samples.
9. The method of claim 1 , wherein the efficiency related value is the maximum gradient of the log of the amplification response.
10. The method of claim 1 , wherein the efficiency related value is the maximum ratio of the amplification response.
11. The method of claim 1 , wherein the efficiency related value is the maximum first derivative of the amplification response.
12. The method of claim 1 , wherein the efficiency related value is the maximum shifted ratio transform of the amplification response.