Differential Dissociation and Melting Curve Peak Detection

• US 20090037117A1
• Filed: 01/25/2008
• Published: 02/05/2009
• Est. Priority Date: 01/30/2007
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Cheng, Francis T.
• Application Number:
  US12/020,369
• Publication Number:
  US 20090037117A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• 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: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 99/00 Subject matter not provided for in other groups of this subclass

Abstract

Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.

Claims

1. A method for determining the differential dissociation curve of at least one sample, comprising:

interpolating emission measurement data of the at least one sample taken at uneven temperature intervals into data at equally-spaced temperature intervals; and

generating a differential dissociation curve by generating a derivative of the emission measurement data.

2. The method of claim 1, further comprising detecting at least one peak in the differential dissociation curve.

3. The method of claim 1, further comprising modifying the differential dissociation curve.

4. The method of claim 1, further comprising generating a power spectrum of the interpolated emission measurement data.

5. The method of claim 1, wherein the derivative comprises a first-order derivative.

6. The method of claim 1, further comprising performing a frequency-domain transform on the interpolated emission measurement data.

7. The method of claim 1, wherein the at least one sample comprises a plurality of samples each having associated emission measurement data.

8. A system for determining the differential dissociation curve of at least one sample, comprising:

an input unit for receiving emission data of at least one sample taken at uneven temperature intervals; and

a processor, communicating with the input unit, the processor being configured to

interpolate the emission measurement data of the at least one sample taken at uneven temperature intervals into data at equally-spaced temperature intervals, and

generate a differential dissociation curve by generating a derivative of the emission measurement data.

9. The system of claim 8, wherein the processor is further configured to detect at least one peak in the differential dissociation curve.

10. The system of claim 8, wherein the processor is further configured to modify the differential dissociation curve.

11. The system of claim 10, wherein the modifying comprises removing emission measurement data associated with peaks that fall below a peak detection threshold.

12. A differential dissociation curve generated for at least one sample, the differential dissociation curve being generated by a method comprising:

interpolating emission measurement data of the at least one sample taken at uneven temperature intervals into data at equally-spaced temperature intervals; and

generating a differential dissociation curve by generating a derivative of the emission measurement data.

13. The differential dissociation curve of claim 12, wherein the method further comprises generating a power spectrum of the interpolated emission measurement data.

14. The differential dissociation curve of claim 13, wherein generating a power spectrum comprises generating a normalized variance of the power spectrum and removing the emission measurement data of the at least one sample when the normalized variance of the power spectrum exceeds a predetermined threshold.

15. A computer-readable medium, the computer-readable medium being readable to execute a method for determining the differential dissociation curve of at least one sample, the method comprising:

interpolating emission measurement data of the at least one sample taken at uneven temperature intervals into data at equally-spaced temperature intervals; and

generating a differential dissociation curve by generating a derivative of the emission measurement data.

16. The computer-readable medium of claim 15, wherein the method further comprises modifying the differential dissociation curve.

17. The computer-readable medium of claim 15, wherein the method further comprises generating a power spectrum of the interpolated emission measurement data.

18. The computer-readable medium of claim 15, wherein the derivative comprises a first-order derivative.

19. The computer-readable medium of claim 15, wherein the method further comprises performing a frequency-domain transform on the interpolated emission measurement data.

20. The computer-readable medium of claim 15, wherein the differential dissociation curve is generated in connection with a polymerase chain reaction process.