Systems and methods for determining real-time PCR cycle thresholds using a rotation transformation
AssigneeRoche Molecular Systems, Inc.
InventorRonald T. Kurnik
Life of this patent
Estimating the term…
Abstract
Systems and methods for determining the elbow or Ct value in a real-time, or kinetic, PCR amplification curve data set. The PCR data set may be visualized in a two-dimensional plot of fluorescence intensity vs. cycle number. A rotation transform is applied to the data set to rotate the data about a defined coordinate such as the origin so that the data point representing the Ct value becomes a minimum or a maximum along the intensity axis. The data point representing the elbow or Ct value of the PCR curve is identified, and this data point is then rotated back and the cycle number of the data point is returned or displayed.
Claims21
A computer-implemented method of determining the elbow or cycle threshold (Ct) value in a region of a Polymerase Chain Reaction (PCR) data curve, the method comprising the steps all of which are, implemented in a computer system having a processor, of:
- receiving a PCR data set representing a PCR data curve, said data set including a plurality of data points each having a pair of coordinate values, wherein if viewed in a two-dimensional coordinate system the data set has a region of interest;
- applying a first rotational transformation to at least a portion of the data set including the region of interest comprising an elbow or cycle threshold (Ct) value to produce a transformed data set;
- identifying a data point in the transformed data set having at least one of a minimum coordinate value or a maximum coordinate value;
- applying a second rotational transformation, inverse to the first transformation, to the identified data point;
- and thereafter
- re-determining at least one coordinate value of the identified data point, wherein the re-determined coordinate value of the identified data point represents the Ct value in the PCR data curve.
A tangible computer readable medium that stores code for controlling a processor to determine a cycle threshold (Ct) value in a kinetic Polymerase Chain Reaction (PCR) amplification curve, the code including instructions to:
- receive a data set representing a kinetic PCR amplification curve, said data set including a plurality of data points each having a pair of coordinate values, wherein said data set includes data points in a region of interest which includes the Ct value;
- apply a first rotational transformation to at least the portion of the data set including the region of interest to produce a transformed data set;
- identify a data point in the transformed data set having at least one of a minimum coordinate value or a maximum coordinate value;
- apply a second rotational transformation, inverse to the first transformation, to the identified data point;
- and thereafter
- re-determine at least one coordinate value of the identified data point, wherein the re-determined coordinate value of the identified data point represents the Ct value for the PCR curve.
A real-time Polymerase Chain Reaction (PCR) system, comprising:
- a PCR analysis module that generates a PCR data set representing a PCR amplification curve, said data set including a plurality of data points each having a pair of coordinate values, wherein said data set includes data points in a region of interest which includes a cycle threshold (Ct) value;
- and
- an intelligence module adapted to process the PCR data set to determine the Ct value by:
- applying a first rotational transformation to at least the portion of the data set including the region of interest to produce a transformed data set;
- identifying a data point in the transformed data set having at least one minimum coordinate value;
- applying a second rotational transformation, inverse to the first transformation, to the identified data point;
- and thereafter
- re-determining at least one coordinate value of the identified data point, wherein the re-determined coordinate value of the identified data point represents the Ct value for the PCR curve.
A real-time Polymerase Chain Reaction (PCR) system, comprising:
- a PCR data acquisition device that generates a PCR data set representing a PCR amplification curve, said data set including a plurality of data points each having a pair of coordinate values, wherein said data set includes data points in a region of interest which includes a cycle threshold (Ct) value;
- and
- a processor adapted to receive and to process the PCR data set to determine the Ct value by:
- applying a first rotational transformation to at least the portion of the data set including the region of interest to produce a transformed data set;
- identifying a data point in the transformed data set having at least one minimum coordinate value;
- applying a second rotational transformation, inverse to the first transformation, to the identified data point;
- and thereafter
- re-determining at least one coordinate value of the identified data point, wherein the re-determined coordinate value of the identified data point represents the Ct value for the PCR curve.
Dependencies are inferred from the claim text.