Inter-cluster intensity variation correction and base calling

Patent metadata

Field	Value
Publication number	US-11853396-B2
Application number	US-202318154603-A
Country	US
Kind code	B2
Filing date	Jan 13, 2023
Priority date	Oct 27, 2020
Publication date	Dec 26, 2023
Grant date	Dec 26, 2023

Abstract

The technology disclosed corrects inter-cluster intensity profile variation for improved base calling on a cluster-by-cluster basis. The technology disclosed accesses current intensity data and historic intensity data of a target cluster, where the current intensity data is for a current sequencing cycle and the historic intensity data is for one or more preceding sequencing cycles. A first accumulated intensity correction parameter is determined by accumulating distribution intensities measured for the target cluster at the current and preceding sequencing cycles. A second accumulated intensity correction parameter is determined by accumulating intensity errors measured for the target cluster at the current and preceding sequencing cycles. Based on the first and second accumulated intensity correction parameters, next intensity data for a next sequencing cycle is corrected to generate corrected next intensity data, which is used to base call the target cluster at the next sequencing cycle.

First claim

What is claimed is:

1. A system comprising at least one processor coupled to memory, the memory loaded with computer instructions that, when executed by the at least one processor, implement actions comprising:
accessing, for a target cluster, current channel-specific intensities registered for a current sequencing cycle of a sequencing run and current channel-specific distribution intensities from a base-specific intensity distribution;
determining a set of current accumulated intensity correction parameters for the current sequencing cycle based on the current channel-specific intensities and the current channel-specific distribution intensities;
determining current channel-specific offset coefficients that offset cluster-specific intensity for the current sequencing cycle based on the set of current accumulated intensity correction parameters;
correcting next channel-specific intensities registered for a next sequencing cycle of the sequencing run based on the current channel-specific offset coefficients; and
determining a base call for the target cluster at the next sequencing cycle based on the corrected next channel-specific intensities.

2. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising:
accessing current channel-specific distribution intensities from the base-specific intensity distribution; and
determining the set of current accumulated intensity correction parameters for the current sequencing cycle based further on the current channel-specific distribution intensities.

3. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising accessing the current channel-specific distribution intensities by accessing the current channel-specific distribution intensities relative to different centroids for different bases across sequencing cycles.

4. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising:
determining a current amplification coefficient that scales a cluster-specific intensity based on the set of current accumulated intensity correction parameters; and
correcting the next channel-specific intensities registered for the next sequencing cycle based further on the current amplification coefficient.

5. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising correcting the next channel-specific intensities by correcting the next channel-specific intensities for inter-cluster intensity variation among intensity values from different clusters for respective bases.

6. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising:
determining a set of current intensity correction parameters for the current sequencing cycle based on the current channel-specific intensities and the current channel-specific distribution intensities; and
determining the set of current accumulated intensity correction parameters for the current sequencing cycle by accumulating the set of current intensity correction parameters.

7. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising determining the set of current accumulated intensity correction parameters by further accumulating a set of preceding accumulated intensity correction parameters for a preceding sequencing cycle of the sequencing run.

8. The system of claim 1 , further comprising computer instructions that, when executed by the at least one processor, implement actions comprising determining the set of current accumulated intensity correction parameters for the current sequencing cycle by:
determining a first accumulated intensity correction parameter by accumulating distribution intensities measured for the target cluster at the current sequencing cycle and each of one or more preceding sequencing cycles, each distribution intensity including an intensity value of a centroid of a base-specific intensity distribution to which the target cluster belongs; and
determining a second accumulated intensity correction parameter by accumulating intensity errors measured for the target cluster at the current sequencing cycle and each of the one or more preceding sequencing cycles, each intensity error including a difference between a measured intensity of the target cluster and a corresponding distribution intensity.

9. A non-transitory computer readable storage medium storing computer instructions that, when executed by at least one processor, cause a system to:
access, for a target cluster, current channel-specific intensities registered for a current sequencing cycle of a sequencing run and current channel-specific distribution intensities from a base-specific intensity distribution;
determine a set of current accumulated intensity correction parameters for the current sequencing cycle based on the current channel-specific intensities and the current channel-specific distribution intensities;
determine current channel-specific offset coefficients that offset cluster-specific intensity for the current sequencing cycle based on the set of current accumulated intensity correction parameters;
correct next channel-specific intensities registered for a next sequencing cycle of the sequencing run based on the current channel-specific offset coefficients; and
determine a base call for the target cluster at the next sequencing cycle based on the corrected next channel-specific intensities.

10. The non-transitory computer readable storage medium of claim 9 , further storing computer instructions that, when executed by the at least one processor, cause the system to:
access current channel-specific distribution intensities from the base-specific intensity distribution; and
determine the set of current accumulated intensity correction parameters for the current sequencing cycle based further on the current channel-specific distribution intensities.

11. The non-transitory computer readable storage medium of claim 9 , further storing computer instructions that, when executed by the at least one processor, cause the system to access the current channel-specific distribution intensities by accessing the current channel-specific distribution intensities relative to different centroids for different bases across sequencing cycles.

12. The non-transitory computer readable storage medium of claim 9 , further storing computer instructions that, when executed by the at least one processor, cause the system to:
determine a current amplification coefficient that scales a cluster-specific intensity based on the set of current accumulated intensity correction parameters; and
correct the next channel-specific intensities registered for the next sequencing cycle based further on the current amplification coefficient.

13. The non-transitory computer readable storage medium of claim 9 , further storing computer instructions that, when executed by the at least one processor, cause the system to correct the next channel-specific intensities by correcting the next channel-specific intensities for inter-cluster intensity variation among intensity values from different clusters for respective bases.

14. The non-transitory computer readable storage medium of claim 9 , further storing computer instructions that, when executed by the at least one processor, cause the system to:
determine

Assignees

• Illumina Inc

Inventors

• Ojard Eric Jon
• Kagalwalla Abde Ali Hunaid
• Mehio Rami
• Udpa Nitin
• Parnaby Gavin Derek
• Vieceli John S

Classifications

• G06F18/2411 Primary

  based on the proximity to a decision surface, e.g. support vector machines · CPC title

• G06F18/21355

  nonlinear criteria, e.g. embedding a manifold in a Euclidean space · CPC title

• G06T7/187

  involving region growing; involving region merging; involving connected component labelling · CPC title

• G06V10/507

  Summing image-intensity values; Histogram projection analysis · CPC title

• G16B40/10 Primary

  Signal processing, e.g. from mass spectrometry [MS] or from PCR · CPC title