Methods for estimating target nucleic acid in a sample prior to amplification by quantitative polymerase chain reaction
AssigneeQuest Diagnostics Investments Incorporated
InventorBenedict G. Archer
Life of this patent
Estimating the term…
Abstract
Provided are methods for estimating the amount of initial target nucleic acid in a sample prior to nucleic acid amplification by polymerase chain reaction (PCR). The methods generally involve modeling signal intensity data generated across a range of PCR cycles with a phenomenological model in concert with a chemical model, to yield an estimate of the amount of initial target nucleic acid in the sample.
Claims29
A method of estimating the amount of initial target nucleic acid in a sample prior to nucleic acid amplification by polymerase chain reaction (PCR), said method comprising:
- modeling signal intensity data generated across a range of PCR cycles with a phenomenological model in concert with a chemical model, to yield an estimate of the amount of initial target nucleic acid in the sample;
- and
- outputting an estimate of the amount of initial target nucleic acid in the sample to a user or computer readable format;
- wherein in the phenomenological model, signal intensity is a function of background, initial target nucleic acid, and amplification efficiency for one or more cycles defined as the fractional amount of target nucleic acid in a reaction mixture generated in a given PCR cycle;
- and in the chemical model, the amount of target nucleic acid generated in a reaction mixture in a given PCR cycle is estimated from kinetic or equilibrium modeling of chemical reactions occurring in the given PCR cycle.
A method of estimating initial target nucleic acid in a sample prior to nucleic acid amplification by polymerase chain reaction (PCR) analysis, said method comprising:
- modeling signal intensity data generated across a range of PCR cycles with a phenomenological model in concert with a chemical model, to yield an estimate of the amount of initial target nucleic acid in the sample, wherein:
- the phenomenological model is a phenomenological model that can be expressed as formula (1);
- and
- the chemical model is a chemical model that can be expressed as a formula selected from the group consisting of formulas (3), (5), and (7).
A computer program product embodied on a computer-readable medium, the computer program product comprising:
- computer code for receiving input indicative of an amount of target nucleic acid present in a sample at a multiple times during a PCR amplification;
- computer code for estimating the initial target nucleic acid in the sample;
- and
- computer code for outputting the estimate of initial target nucleic acid in the sample to a user or computer readable media;
- wherein, the computer code for estimating the initial target nucleic acid operates in accordance with formula (2) and a formula selected from the group consisting of formulas (3), (5), and (7).
An apparatus, comprising:
- a processor;
- and
- a memory unit coupled to the processor and including:
- computer code for receiving input indicative of amount of target nucleic acid present in a sample at multiple times during a PCR amplification;
- computer code for estimating the initial target nucleic acid in the sample;
- and
- computer code for outputting the estimate of initial target nucleic acid in the sample to a user or computer readable media;
- wherein, the computer code for estimating the initial target nucleic acid operates in accordance with formula (2) and a formula selected from the group consisting of formulas (3), (5), and (7).
Dependencies are inferred from the claim text.