Analysis of nucleic acid amplification curves using wavelet transformation

1. A method comprising:

performing a PCR analysis of a nucleic acid sample, wherein the PCR analysis comprises a plurality of PCR cycles;

from the PCR analysis, acquiring amplification data proportional to an amount of nucleic acid present for each of the plurality of PCR cycles;

applying wavelet transformation to the amplification data to determine a PCR cycle corresponding to a point within a growth period of the amplification data; and

updating a display based on the PCR cycle corresponding to a point within a growth period of the amplification data.

2. The method of claim 1 , wherein applying wavelet transformation comprises:

generating an amplification curve from the amplification data, the amplification curve representing growth of the nucleic acid sample versus PCR cycle; and

applying continuous wavelet transformation (CWT) to the amplification curve to decompose the amplification curve into frequency components while maintaining PCR cycle localization for the frequency components along the amplification curve.

3. The method of claim 1 ,

wherein the amplification data represents growth of the nucleic acid sample over time, and

wherein applying wavelet transformation comprises applying discrete wavelet transformation (DWT) to the amplification data to decompose the amplification data into frequency components while maintaining PCR cycle localization for the frequency components with respect to time.

4. The method of claim 1 , wherein the PCR cycle corresponding to a point within a growth period of the amplification data comprises a fraction of a PCR cycle.

5. The method of claim 1 , wherein the PCR cycle corresponding to a point within a growth period of the amplification data is referred to as a T max value.

6. The method of claim 1 , wherein the PCR cycle corresponding to a point within a growth period of the amplification data corresponds to an approximate onset of the growth period.

7. The method of claim 1 , wherein updating a display comprises displaying a message based on the PCR cycle corresponding to a point within a growth period of the amplification data.

8. The method of claim 5 , wherein updating a display comprises displaying the T max value.

9. The method of claim 5 , wherein the nucleic acid sample comprises a known initial nucleic acid concentration.

10. The method of claim 9 , wherein updating a display comprises displaying the T max value on a plot comprising the T max value versus a logarithm of the initial nucleic acid concentration.

11. The method of claim 10 , further comprising:

repeating the method of claim 1 for each of a plurality of nucleic acid samples each comprising a known initial nucleic acid concentration.

12. The method of claim 11 , wherein the plot further comprises a standard curve fit to the T max values versus logarithm of the initial nucleic acid concentration for each of the plurality of samples using linear regression.

13. The method of claim 12 , further comprising:

repeating the method of claim 1 for a nucleic acid sample comprising an unknown initial nucleic acid concentration.

14. The method of claim 13 , wherein updating a display comprises displaying a T max value of the nucleic acid sample comprising an unknown initial nucleic acid concentration on the plot.

15. The method of claim 14 , further comprising:

determining the initial amount of nucleic acid in the nucleic acid sample comprising an unknown initial nucleic acid concentration based on the T max value of the nucleic acid sample comprising an unknown initial nucleic acid concentration and the standard curve.

16. The method of claim 5 , wherein the nucleic acid sample comprises an unknown initial nucleic acid concentration.

17. The method of claim 16 , further comprising:

determining an initial concentration of the nucleic acid sample based on the T max value and a standard curve.

18. The method of claim 5 , wherein applying wavelet transformation to the amplification data comprises generating a plurality of frequency slices, wherein each of the plurality of frequency slices comprises a plurality of time translation values and wherein each time translation value comprises a wavelet transformation magnitude.

19. The method of claim 18 , wherein applying wavelet transformation to the amplification data comprises determining the T max value based on the wavelet transformation magnitude of at least one of the plurality of time translation values.

20. The method of claim 1 , wherein applying wavelet transformation to the amplification data comprises applying a Haar wavelet in wavelet transformation to the amplification data.

21. The method of claim 1 , wherein applying wavelet transformation to the amplification data comprises selecting a wavelet.

22. The method of claim 18 , wherein applying wavelet transformation to the amplification data comprises selecting one of the plurality of frequency slices and determining the T max value based on the wavelet transformation magnitude of at least one of the plurality of time translation values in the frequency slice.

23. A computer-readable medium comprising instructions that cause a processor to:

initiate a PCR analysis of a nucleic acid sample, wherein the PCR analysis comprises a plurality of PCR cycles;

from the PCR analysis, receive amplification data proportional to an amount of nucleic acid present for each of the plurality of PCR cycles;

apply wavelet transformation to the amplification data to determine a PCR cycle corresponding to a point within a growth period of the amplification data; and

update a display based on the PCR cycle corresponding to a point within a growth period of the amplification data.

24. The computer-readable medium of claim 23 , wherein the nucleic acid sample comprises an unknown initial amount of nucleic acid, and wherein the computer-readable medium further comprises instructions to cause a processor to:

determine an initial concentration of the nucleic acid sample based on the PCR cycle corresponding to a point within a growth period of the amplification data and a standard curve.

25. A device comprising:

a control module that initializes a PCR analysis of a nucleic acid sample and receives amplification data proportional to an amount of nucleic acid present for each of a plurality of PCR cycles;

an analysis module that applies wavelet transformation to the amplification data and identifies components having the largest local wavelet magnitudes of the transformed amplification data to determine a PCR cycle corresponding to a point within a growth period of the amplification data; and

an interface module that updates a display based on the PCR cycle corresponding to a point within a growth period of the amplification data.

26. The device of claim 25 , wherein the analysis module:

generates an amplification curve from the amplification data, the amplification curve representing growth of the nucleic acid sample versus PCR cycle; and

applies continuous wavelet transformation (CWT) to the amplification curve to decompose the amplification curve into frequency components while maintaining PCR cycle localization for the frequency components along the amplification curve.

27. The device of claim 25 ,

wherein the amplification data represents growth of the nucleic acid sample over time, and

wherein the analysis module applies discrete wavelet transformation (DWT) to the amplification data to decompose the amplification data into frequency components while maintaining PCR cycle localization for the frequency components with respect to time.

28. The device of claim 25 , wherein the PCR cycle corresponding to a point within a growth period of the amplification data comprises a fraction of a cycle.

29. The device of claim 25 , wherein the PCR cycle corresponding to a point within a growth period of the amplification data is referred to as a T max value.

30. The device of claim 25 , wherein the PCR cycle corresponding to a point within a growth period of the amplification data corresponds to an approximate onset of the growth period.

31. The device of claim 25 , wherein the interface module displays a message based on the PCR cycle corresponding to a point within a growth period of the amplification data.

32. The device of claim 29 , wherein the interface module displays the T max value.

33. The device of claim 25 , further comprising a database module to store the amplification data.

34. The device of claim 29 , wherein the nucleic acid sample comprises a known initial amount of nucleic acid.

35. The device of claim 34 , wherein the interface module displays the T max value on a plot comprising the T max versus a logarithm of the initial amount of nucleic acid.

36. The device of claim 35 , wherein the analysis module determines a T max value for each of a plurality of nucleic acid samples comprising a known initial amount of nucleic acid.

37. The device of claim 36 , wherein the plot further comprises a line fit to the T max value versus logarithm of the initial amount of nucleic acid for each of the plurality of samples using linear regression.

38. The device of claim 37 , wherein the analysis module determines a T max value for a nucleic acid sample comprising an unknown initial amount of nucleic acid.

39. The device of claim 38 , wherein the interface module displays the T max value of the nucleic acid sample comprising an unknown initial amount of nucleic acid on the plot.

40. The device of claim 39 , wherein the analysis module determines the initial amount of nucleic acid in the nucleic acid sample comprising an unknown initial amount of nucleic acid based on the T max value of the nucleic acid sample comprising an unknown initial amount of nucleic acid and the line.

41. The device of claim 29 , wherein the nucleic acid sample comprises an unknown initial amount of nucleic acid.

42. The device of claim 41 , wherein the analysis module determines an initial concentration of the nucleic acid sample based on the T max value and a standard curve.

43. The device of claim 29 , wherein the analysis module applies wavelet transformation to the amplification data to generate a plurality of frequency slices, wherein each of the plurality of frequency slices comprises a plurality of time translation values and wherein each time translation value comprises a wavelet amplitude.

44. The device of claim 43 , wherein the analysis module determines a T max value based on the wavelet amplitude of at least one of the plurality of time translation values.

45. The device of claim 25 , wherein the analysis module applies a Haar wavelet to the amplification data.

46. The device of claim 25 , wherein applying wavelet transformation to the amplification data comprises selecting a wavelet.

47. The device of claim 43 , wherein the analysis module selects one of the plurality of frequency slices and determines a T max value based on the wavelet transformation magnitude of at least one of the plurality of time translation values in the frequency slice.