PCR elbow determination using curvature analysis of a double sigmoid

A technology of maximum curvature and curve, applied in the field of PCR elbow determination using double S-shaped curvature analysis, can solve problems such as unsatisfactory work and unsuitable data sets

Active Publication Date: 2010-12-08
F HOFFMANN LA ROCHE & CO AG
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

For example, some methods are sensitive to abnormal (noisy) data, and the AFL value method is not suitable for datasets with high baseline
Especially in the case of high titers, it is used to determine figure 1 The traditional approach of the baseline stop (or the end point of the baseline) of the growth curve shown in does not work satisfactorily

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  • PCR elbow determination using curvature analysis of a double sigmoid
  • PCR elbow determination using curvature analysis of a double sigmoid
  • PCR elbow determination using curvature analysis of a double sigmoid

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Embodiment Construction

[0050] The present invention provides systems and methods for determining transition values ​​in a sigmoid or growth curve, such as the end of a baseline region or the elbow or Ct value of a PCR amplification curve. In certain aspects, a double sigmoid function with parameters determined by the Levenberg-Marquardt (LM) regression method is used to find an approximation to the curve. Once the parameters have been determined, the curve can be normalized using one or more of the determined parameters. After normalization, the normalized curve is processed to determine the curvature of the curve at some or all points along the curve, eg, to produce a data set or graph representing curvature versus cycle number. The number of cycles where the greatest curvature occurs corresponds to this Ct value. This Ct value is then returned and may be displayed or otherwise used for further processing.

[0051] exist figure 1 An example of a growth or amplification curve 10 in the context of...

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Abstract

Systems and methods for determining characteristic transition values such as elbow values in sigmoid or growth-type curves, such as the cycle threshold (Ct) value in PCR amplification curves. A double sigmoid function with parameters determined by a Levenberg-Marquardt (LM) regression process is used to find an approximation to a curve that fits a PCR dataset. Once the parameters have been determined, the curve can be normalized using one or more of the determined parameters. After normalization, the normalized curve is processed to determine the curvature of the curve at some or all points along the curve, e.g., to produce a dataset or plot representing the curvature v. the cycle number. The cycle number at which the maximum curvature occurs corresponds to the Ct value. The Ct value is then returned and may be displayed or otherwise used for further processing.

Description

[0001] This application is a divisional application of the application number 200610169374.1, the application date is December 19, 2006, and the invention title is "PCR Elbow Determination Using Double S-shaped Curvature Analysis". technical field [0002] The present invention relates broadly to systems and methods for processing data representing sigmoid curves or growth curves, and more particularly to methods for determining characteristic cycle thresholds (Ct) or elbow values ​​or Systems and methods for elbow values ​​in other growth curves. Background technique [0003] Polymerase chain reaction (PCR) is an ex vivo method for enzymatic synthesis or amplification of defined nucleic acid sequences. The reaction typically utilizes two oligonucleotide primers that hybridize to opposing strands and flank the template or target DNA sequence to be amplified. Extension of these primers is catalyzed by thermostable DNA polymerases. A series of repeated cycles involving denat...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F17/17C12Q1/68G06K9/00
CPCG06F17/17G06K9/0053C12Q1/6851G06F17/10G06F2218/10C12Q2537/165
Inventor R·T·库尔尼克J·王
Owner F HOFFMANN LA ROCHE & CO AG
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