# US 12,216,741 B2 · Inter-cluster intensity variation correction and base calling

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- Number: US 12,216,741 B2
- Document ID: US12216741B2
- Status: Granted
- Kind: B2
- Application number: 18/501,904
- Filed: 2023-11-03
- Published: 2024-07-04
- Granted: 2025-02-04
- Earliest claimed: 2020-10-27
- Assignees: Illumina, Inc.
- Applicants: Illumina, Inc.
- Inventors: Eric Jon Ojard; Abde Ali Hunaid Kagalwalla; Rami Mehio; Nitin Udpa; Gavin Derek Parnaby; John S. Vieceli
- Web page: https://patentgrep.com/patent/US12216741B2

## CPC

- G06F 18/2411: based on the proximity to a decision surface, e.g. support vector machines
- G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR
- G06F 18/21355: {nonlinear criteria, e.g. embedding a manifold in a Euclidean space}
- G06T 7/187: involving region growing; involving region merging; involving connected component labelling
- G06V 10/507: {Summing image-intensity values; Histogram projection analysis}
- G16B 40/30: Unsupervised data analysis
- G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G06T: IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06V: IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING

## 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.

## Claims

### Claim 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 intensities registered from the target cluster and other clusters for a current sequencing cycle;
determining a set of current accumulated intensity correction parameters for the current sequencing cycle based on the current intensities;
determining, for the target cluster and based on the set of current accumulated intensity correction parameters, a current amplification coefficient;
correcting next intensities registered for a next sequencing cycle based on the current amplification coefficient; and
determining a base call for the target cluster at the next sequencing cycle based on the corrected next intensities.

### Claim 2 (depends on 1)

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

### Claim 3 (depends on 2)

The system of claim 2, wherein:
the current intensities comprise current channel-specific intensities registered for the current sequencing cycle; and
the current distribution intensities comprise current channel-specific distribution intensities from the base-specific intensity distribution.

### Claim 4 (depends on 1)

The system of claim 1, wherein the current amplification coefficient scales the current intensities for the target cluster relative to intensities of the other clusters on a flow cell.

### Claim 5 (depends on 1)

The system of claim 1, wherein the current amplification coefficient scales the current intensities for the target cluster relative to channel-specific intensities or cluster-specific intensities of the other clusters on a flow cell.

### Claim 6 (depends on 1)

The system of claim 1, further comprising computer instructions that, when executed by the at least one processor, implement actions comprising:
combining an initial amplification coefficient with the current amplification coefficient to generate a modified current amplification coefficient; and
correcting the next intensities registered for the next sequencing cycle based on the modified current amplification coefficient.

### Claim 7 (depends on 6)

The system of claim 6, further comprising computer instructions that, when executed by the at least one processor, implement actions comprising combining the initial amplification coefficient with the current amplification coefficient to generate the modified current amplification coefficient by:
applying, utilizing a weighting function, a first weight to the initial amplification coefficient;
applying, utilizing the weighting function, a second weight to the current amplification coefficient; and
generating a weighted current amplification coefficient based on the first weighted initial amplification coefficient and the second weighted current amplification coefficient.

### Claim 8 (depends on 6)

The system of claim 6, further comprising computer instructions that, when executed by the at least one processor, implement actions comprising combining the initial amplification coefficient with the current amplification coefficient to generate the modified current amplification coefficient by:
applying, utilizing a weighting function, a minimum weight (wmin) to the initial amplification coefficient;
applying, utilizing the weighting function, a maximum weight (wmax) to the current amplification coefficient; and
generating a weighted current amplification coefficient based on the minimum weighted initial amplification coefficient and the maximum weighted current amplification coefficient.

### Claim 9 (depends on 1)

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

### Claim 10 (depends on 1)

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

### Claim 11

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 intensities registered from the target cluster and other clusters for a current sequencing cycle;
determine a set of current accumulated intensity correction parameters for the current sequencing cycle based on the current intensities;
determine, for the target cluster and based on the set of current accumulated intensity correction parameters, a current amplification coefficient;
correct next intensities registered for a next sequencing cycle based on the current amplification coefficient; and
determine a base call for the target cluster at the next sequencing cycle based on the corrected next intensities.

### Claim 12 (depends on 11)

The non-transitory computer readable storage medium of claim 11, further storing computer instructions that, when executed by the at least one processor, cause the system to:
access, for the target cluster, current distribution intensities from a base-specific intensity distribution; and
determine the set of current accumulated intensity correction parameters for the current sequencing cycle further based on the current distribution intensities.

### Claim 13 (depends on 11)

The non-transitory computer readable storage medium of claim 11, wherein the current amplification coefficient scales the current intensities for the target cluster relative to intensities of the other clusters on a flow cell.

### Claim 14 (depends on 11)

The non-transitory computer readable storage medium of claim 11, wherein the current amplification coefficient scales the current intensities for the target cluster relative to channel-specific intensities or cluster-specific intensities of the other clusters on a flow cell.

### Claim 15 (depends on 11)

The non-transitory computer readable storage medium of claim 11, further storing computer instructions that, when executed by the at least one processor, cause the system to:
combine an initial amplification coefficient with the current amplification coefficient to generate a modified current amplification coefficient; and
correct the next intensities registered for the next sequencing cycle based on the modified current amplification coefficient.

### Claim 16 (depends on 15)

The non-transitory computer readable storage medium of claim 15, further storing computer instructions that, when executed by the at least one processor, cause the system to combine the initial amplification coefficient with the current amplification coefficient to generate the modified current amplification coefficient by:
applying, utilizing a weighting function, a first weight to the initial amplification coefficient;
applying, utilizing the weighting function, a second weight to the current amplification coefficient; and
generating a weighted current amplification coefficient based on the first weighted initial amplification coefficient and the second weighted current amplification coefficient.

### Claim 17 (depends on 15)

The non-transitory computer readable storage medium of claim 15, further storing computer instructions that, when executed by the at least one processor, cause the system to combine the initial amplification coefficient with the current amplification coefficient to generate the modified current amplification coefficient by:
applying, utilizing a weighting function, a minimum weight (wmin) to the initial amplification coefficient;
applying, utilizing the weighting function, a maximum weight (wmax) to the current amplification coefficient; and
generating a weighted current amplification coefficient based on the minimum weighted initial amplification coefficient and the maximum weighted current amplification coefficient.

### Claim 18

A computer-implemented method comprising:
accessing, for a target cluster, current intensities registered from the target cluster and other clusters for a current sequencing cycle;
determining a set of current accumulated intensity correction parameters for the current sequencing cycle based on the current intensities;
determining, for the target cluster and based on the set of current accumulated intensity correction parameters, a current amplification coefficient;
correcting next intensities registered for a next sequencing cycle based on the current amplification coefficient; and
determining a base call for the target cluster at the next sequencing cycle based on the corrected next intensities.

### Claim 19 (depends on 18)

The computer-implemented method of claim 18, further comprising:
determining offset coefficients that offset cluster-specific intensity for the current sequencing cycle based on the set of current accumulated intensity correction parameters; and
correcting, for the next sequencing cycle, the next intensities registered based on the current amplification coefficient and the offset coefficients.

### Claim 20 (depends on 18)

The computer-implemented method of claim 18, wherein correcting the next intensities comprises correcting, for the next sequencing cycle, the next intensities for inter-cluster intensity variation among intensity values from different clusters for respective bases.