Models for analyzing data from sequencing-by-synthesis operations

• US 9,646,132 B2
• Filed: 05/10/2013
• Issued: 05/09/2017
• Est. Priority Date: 05/11/2012
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Rearick, Todd
• Primary Examiner(s): NEGIN, RUSSELL SCOTT
• Application Number:
  US13/892,116
• Publication Number:
  US 20130303384A1
• Time in Patent Office: 1,460 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2563/113 the label being electroactive, e.g. redox labels
• CPC Class Codes: C12Q 2563/116 electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks

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.

Claims

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, the output signals being generated by the reactor array during the flowing of the series of nucleotide flows in response to chemical changes occurring in at least some of the reaction confinement regions;

estimating a background signal component of the received output signals for the loaded reaction confinement region using at least 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, the headspace being located adjacent to and above the loaded reaction confinement region and the one or more neighboring reaction confinement regions such that a bulk fluid, the loaded confinement region, and the one or more neighboring reaction confinement regions are modeled to exchange ions with each other through the headspace, wherein the background model is derived using a first characteristic equation that comprises a term related to a difference between a proton concentration in the loaded reaction confinement region and a proton concentration in the headspace; and

fitting an output signal model based on at least the estimated background signal component to the signal data, wherein the fitting is used to generate sequence data representative of nucleotide incorporations into the copies of the polynucleotide strands resulting from the series of nucleotide flows.

2. The method of claim 1, wherein the background model represents at least an exchange of ions between at least two neighboring reaction confinement regions and the headspace.

3. The method of claim 1, wherein the background model represents at least an exchange of ions between at least three neighboring reaction confinement regions and the headspace.

4. The method of claim 1, wherein the background model represents at least an exchange of ions between at least four neighboring reaction confinement regions and the headspace.

5. The method of claim 1, wherein the background model represents at least an exchange of ions between six neighboring reaction confinement regions and the headspace, the six neighboring reaction confinement regions being arranged hexagonally around the loaded reaction confinement region.

6. The method of claim 1, wherein the background model simulates a relationship between the loaded reaction confinement region, the neighboring reaction confinement regions, and the bulk fluid, all interacting with each other through the headspace.

7. The method of claim 1, wherein the background model represents at least an exchange of ions between the headspace and the bulk fluid.

8. The method of claim 1, wherein the first characteristic equation represents a conservation of protons in the headspace.

9. The method of claim 8, wherein the first characteristic equation is:

10. The method of claim 8, 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.

11. The method of claim 8, wherein the first characteristic equation comprises a term related to a difference between a proton concentration in the bulk fluid and a proton concentration in the headspace.

12. The method of claim 8, wherein the background model is further derived using a second characteristic equation representing conservation of protons in the loaded reaction confinement region.

13. The method of claim 12, wherein the second characteristic equation is:

14. The method of claim 1, wherein the background model comprises an interaction equation representing a relationship between the loaded reaction confinement region, the neighboring reaction confinement regions, and the bulk fluid, all interacting with each other through the headspace.

15. The method of claim 14, wherein the interaction equation is:

16. The method of claim 1, wherein the background model comprises a simplified equation representing a relationship between the loaded reaction confinement region, the neighboring reaction confinement regions, and the bulk fluid, all interacting with each other through the headspace, the simplified equation being:

17. A non-transitory machine-readable storage medium comprising instructions which, when executed by a processor, cause the processor to:

receive output signals generated in response to a flow of a series of nucleotides 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, wherein the output signals are generated by the reactor array during the flowing of the series of nucleotide flows in response to chemical changes occurring in at least some of the reaction confinement regions;

estimate a background signal component of the received output signals for the loaded reaction confinement region using at least 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, the headspace being located adjacent to and above the loaded reaction confinement region and the one or more neighboring reaction confinement regions such that a bulk fluid, the loaded confinement region, and the one or more neighboring reaction confinement regions are modeled to exchange ions with each other through the headspace, wherein the background model is derived using a first characteristic equation that 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; and

fit an output signal model to the based on at least the modeled background signal to the signal data, wherein the fitting is used to generate sequence data representative of nucleotide incorporations into the copies of the polynucleotide strands resulting from the series of nucleotide flows.

18. The non-transitory machine-readable storage medium of claim 17, wherein the background model represents at least an exchange of ions between six neighboring reaction confinement regions and the headspace, the six neighboring reaction confinement regions being arranged hexagonally around the loaded reaction confinement region.

19. 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, the output signals being generated by the reactor array during the flowing of the series of nucleotide flows in response to chemical changes occurring in at least some of the reaction confinement regions;

estimating a background signal component of the received output signals for the loaded reaction confinement region using at least 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, the headspace being located adjacent to and above the loaded reaction confinement region and the one or more neighboring reaction confinement regions such that a bulk fluid, the loaded confinement region, and the one or more neighboring reaction confinement regions are modeled to exchange ions with each other through the headspace, wherein the background model is derived using a first characteristic equation that comprises a term related to a difference between a proton concentration in the loaded reaction confinement region and a proton concentration in the headspace; and

fitting an output signal model based on at least the estimated background signal component to the signal data, wherein the fitting is used to generate sequence data representative of nucleotide incorporations into the copies of the polynucleotide strands resulting from the series of nucleotide flows.