Differential dissociation and melting curve peak detection

• US 9,977,860 B2
• Filed: 04/22/2014
• Issued: 05/22/2018
• Est. Priority Date: 01/30/2007
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Cheng, Francis T.
• Primary Examiner(s): HARWARD, SOREN T
• Application Number:
  US14/259,057
• Publication Number:
  US 20140343862A1
• Time in Patent Office: 1,491 Days
• Field of Search: None
• 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 biological substance analysis, the method comprising:

physically dissociating at least one sample of the biological substance by progressively changing a temperature of the at least one sample;

operating an emission detector to measure intensities of light emitted from a dye bound to the at least one sample as the temperature is progressively changed, thus producing measured intensities of light, wherein the dye remains bound to the at least one sample until the at least one sample is dissociated;

executing machine instructions by a system processor to cause the system to;

interpolate the measured intensities of light into a set of interpolated intensities for a plurality of temperatures at equally-spaced temperature intervals of the at least one sample including providing a user interface on a machine display to display a plurality of data points comprising the measured intensities of light at corresponding temperatures, the user interface also providing for marking of data points within a user-specified neighborhood or region, around or in proximity to a particular temperature of the plurality of temperatures and the machine instructions further causing the system to apply a weighting function to the marked data points to generate a new data sample value to be included in the set of interpolated intensities;

generate a differential dissociation curve from a derivative of the interpolated intensities;

determine a pedestal using one or more valleys proximate to a particular peak identified in the differential dissociation curve;

generate an adjusted differential dissociation curve by subtracting the pedestal from one or more peaks of the differential dissociation curve; and

generate the adjusted differential dissociation curve on a machine display.

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 set of interpolated intensities.

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 set of interpolated intensities.

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

8. A system for generating a visualization of a differential dissociation curve of at least one sample on a machine display, comprising:

an input unit for receiving, from sensors, emission measurements from at least one sample, the sample comprising a dye that remains bound to the sample until the sample is dissociated; and

a processor, communicating with the input unit, the processor being configured to cause the system to;

receive the emission measurements from the input unit and record the emission measurements at uneven temperature intervals of the sample;

interpolate the emission measurements into a set of interpolated intensities for a plurality of temperatures at equally-spaced temperature intervals of the at least one sample including providing a on a machine display to display a plurality of data points comprising the emission measurements at corresponding temperatures, the user interface also providing for marking of data points within a user-specified neighborhood or region, around or in proximity to a particular temperature of the plurality of temperatures and the machine instructions further causing the system to apply a weighting function to the marked data points to generate a new data sample value to be included in the set of interpolated intensities;

form a differential dissociation curve from a derivative of the set of interpolated intensities;

determine a pedestal using one or more valleys proximate to a particular peak identified in the differential dissociation curve;

generate an adjusted differential dissociation curve by subtracting the pedestal from one or more peaks of the differential dissociation curve; and

form the adjusted differential dissociation curve on the machine display.

9. The system of claim 8, wherein the processor is further configured to cause the system to:

detect at least one peak in the differential dissociation curve.

10. The system of claim 8, wherein the processor is further configured to cause the system to:

modify the differential dissociation curve.

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

12. A computer-readable medium, the computer-readable medium comprising instructions for a computer-implemented method for generating a differential dissociation curve of at least one sample on a machine display, the method comprising:

interfacing with sensors to measure emission intensities of a dye bound to at least one sample, the emission intensities measured at uneven temperature intervals to produce emission measurements, wherein the dye remains bound to the at least one sample until the at least one sample is dissociated and wherein the at least one sample is dissociated by changing the temperature of the at least one sample;

interpolate the emission measurements of the at least one sample into a set of interpolated intensities for a plurality of temperatures at equally-spaced temperature intervals of the at least one sample including providing a user interface on a machine display to display a plurality of data points comprising the emission measurements at corresponding temperatures, the user interface also providing for marking of data points within a user-specified neighborhood or region, around or in proximity to a particular temperature of the plurality of temperatures and the machine instructions further causing the processor to apply a weighting function to the marked data points to generate a new data sample value to be included in the set of interpolated intensities;

generating a differential dissociation curve from a derivative of the interpolated intensities;

determining a pedestal using one or more valleys proximate to a particular peak identified in the differential dissociation curve;

generating an adjusted differential dissociation curve by subtracting the pedestal from one or more peaks of the differential dissociation curve; and

generating the adjusted differential dissociation curve on the machine display.

13. The computer-readable medium of claim 12, wherein the method further comprises:

modifying the differential dissociation curve.

14. The computer-readable medium of claim 12, wherein the method further comprises:

generating a power spectrum of the interpolated emission measurements.

15. The computer-readable medium of claim 12, wherein the derivative of the emission measurements comprises a first-order derivative of the emission measurements.

16. The computer-readable medium of claim 12, wherein the method further comprises performing a frequency-domain transform on the interpolated emission measurements.

17. The computer-readable medium of claim 12, wherein the differential dissociation curve is generated in connection with a polymerase chain reaction process.