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US 11,386,978 B2Granted
Fluidic chemFET polynucleotide sequencing systems with confinement regions and hydrogen ion rate and ratio parameters
AssigneeLife Technologies Corporation
InventorsTodd Rearick, Jonathan Schultz
Life of this patent
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Abstract
Mathematical models for the analysis of signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the measured output signal from the reaction confinement region of a reactor array is mathematically modeled. The output signal may be modeled as a linear combination of one or more signal components, including a background signal component. This model is solved to determine the nucleotide incorporation signal. In another embodiment, the incorporation signal from the reaction confinement region of a reactor array is mathematically modeled.
Claims20
A system for sequencing polynucleotides, the system comprising:
- a sequencing apparatus comprising:
- a plurality of confinement regions configured to receive a sample volume comprising a polynucleotide strand,
- a sensor array comprising a plurality of chemFET sensors respectively aligned with the plurality of confinement regions, and
- a fluidics system configured to flow a series of nucleotide solution flows to the plurality of confinement regions;
- and
- a processor operably coupled to the sequencing apparatus and programmed with instructions configured to cause the processor to:
- receive output signals generated in response to a chemical reaction between the series of nucleotide solution flows and a polynucleotide strand located in a loaded confinement region of the plurality of confinement regions, the output signals being from a chemFET sensor of the plurality of chemFET sensors associated with the loaded confinement region,
- determine a background signal for the loaded confinement region using a model of an output signal from the loaded confinement region, the model of the output signal from the loaded confinement region being a linear combination of a function of a first signal component and a function of a second signal component, wherein to determine the background signal, the model of the output signal from the loaded confinement region is fit to the received output signals based on at least a ratio parameter of the function of the second signal component, wherein:
- the second signal component is generated based on an output signal from an unloaded confinement region of the plurality of confinement regions, and
- the function of the second signal component comprises:
- (i) a rate parameter that varies with a rate of change in an amount of hydrogen ions in the loaded confinement region, and
- (ii) the ratio parameter, the ratio parameter varying with a ratio of a rate of change in the amount of hydrogen ions in the unloaded confinement region relative to the rate of change in the amount of hydrogen ions in the loaded confinement region;
- determine an incorporation signal from the loaded confinement region using the model of the output signal from the loaded confinement region, wherein to determine the incorporation signal, the model is fit to at least some of the received output signals based on one or more parameters of the function of the first signal component, and
- determine an estimate of a number of nucleotides incorporated into the polynucleotide strand using a method selected from (a) using a peak of the determined incorporation signal to estimate the number of nucleotides incorporated, and (b) comparing the determined incorporation signal to a set of reference incorporation signal curves to estimate the number of nucleotides incorporated.
11 more elements
A system for sequencing polynucleotides, the system comprising:
- a sequencing apparatus comprising:
- a plurality of confinement regions, each configured to receive a sample comprising a polynucleotide strand, a sensor array comprising a plurality of chemFET sensors respectively aligned with the plurality of confinement regions, and
- a fluidics system configured to flow a series of nucleotide solution flows to the plurality of confinement regions;
- and
- a processor operably coupled with the sequencing apparatus and programmed with instructions configured to cause the processor to:
- receive output signals generated in response to a chemical reaction between the series of nucleotide solution flows and a polynucleotide strand located in a loaded confinement region of the plurality of confinement regions, the output signals being from a chemFET sensor of the plurality of chemFET sensors associated with the loaded confinement region,
- fit an incorporation signal model comprising a system of non-linear differential equations to the output signals, the system of non-linear differential equations comprising a first equation representing a rate of change in a nucleotide concentration in the loaded confinement region and a second equation representing an amount of active polymerase in the loaded confinement region;
- and
- determine, from the fit of the incorporation signal model, an estimate of a number of nucleotide incorporations resulting from the series of nucleotide solution flows.
6 more elements
Dependencies are inferred from the claim text.