Models for analyzing data from sequencing-by-synthesis operations
First Claim
1. A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis, comprising:
- flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions;
receiving output signals from the reactor array; and
estimating a background signal for the loaded reaction confinement region using the received output signals and a background model representing at least an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent to the loaded reaction confinement region and the one or more neighboring reaction confinement regions, wherein the background model is derived using a first characteristic equation, wherein the first characteristic equation comprises a term related to a difference between a proton concentration in each of the neighboring reaction confinement regions and a proton concentration in the headspace.
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Abstract
A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis includes: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions that may or may not be loaded; receiving output signals from the reactor array; and modeling a background signal for the loaded reaction confinement region using the received output signals and a model adapted to account at least for an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent the loaded reaction confinement region and the one or more neighboring reaction confinement regions.
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Citations
20 Claims
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1. A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis, comprising:
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flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions; receiving output signals from the reactor array; and estimating a background signal for the loaded reaction confinement region using the received output signals and a background model representing at least an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent to the loaded reaction confinement region and the one or more neighboring reaction confinement regions, wherein the background model is derived using a first characteristic equation, wherein the first characteristic equation comprises a term related to a difference between a proton concentration in each of the neighboring reaction confinement regions and a proton concentration in the headspace. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A non-transitory machine-readable storage medium comprising instructions which, when executed by a processor, cause the processor to:
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receive output signals relating to chemical reactions resulting from the flow of a series of nucleotides onto a reactor array having multiple reaction confinement regions, one or more copies of a polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions; and estimate a background signal for the loaded reaction confinement region using the received output signals and a background model representing at least an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent to the loaded reaction confinement region and the one or more neighboring reaction confinement regions, wherein the background model is derived using a first characteristic equation, wherein the first characteristic equation comprises a term related to a difference between a proton concentration in each of the neighboring reaction confinement regions and a proton concentration in the headspace. - View Dependent Claims (19, 20)
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Specification