Inter-cluster intensity variation correction and base calling

Patent metadata

Field	Value
Publication number	US-11593595-B2
Application number	US-202217752789-A
Country	US
Kind code	B2
Filing date	May 24, 2022
Priority date	Oct 27, 2020
Publication date	Feb 28, 2023
Grant date	Feb 28, 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 computer-implemented method of base calling a target cluster, the computer-implemented method comprising:
accessing current intensity data and historic intensity data of the target cluster;
wherein the current intensity data is for a current sequencing cycle of a sequencing run, and
wherein the historic intensity data is for one or more preceding sequencing cycles of the sequencing run,

determining a first accumulated intensity correction parameter by accumulating distribution intensities measured for the target cluster at the current sequencing cycle and each of the 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;
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;
correcting, based on the first and second accumulated intensity correction parameters, next intensity data to generate corrected next intensity data,
wherein the next intensity data is for a next sequencing cycle of the sequencing run; and

base calling the target cluster at the next sequencing cycle based on the corrected next intensity data.

2. The computer-implemented method of claim 1 , wherein the first and second accumulated intensity correction parameters are used to generate a scale correction coefficient and a shift correction coefficient corresponding to the current sequencing cycle.

3. The computer-implemented method of claim 2 , wherein the shift correction coefficient is subtracted from the next intensity data to generate a shifted next intensity data, and the shifted next intensity data is divided by the scale correction coefficient to generate the corrected next intensity data.

4. The computer-implemented method of claim 1 , wherein each of the distribution intensities at a corresponding sequencing cycle is determined from a centroid of a base-specific intensity distribution to which the target cluster belongs in a corresponding intensity channel.

5. The computer-implemented method of claim 1 , wherein each of the intensity errors at a corresponding sequencing cycle is determined as a difference between a measured intensity value of the target cluster and a distribution intensity in a corresponding intensity channel.

6. The computer-implemented method of claim 1 , further comprising:
reading a current intensity registered for the current sequencing cycle from a base-specific intensity distribution to which the target cluster is base called at the current sequencing cycle;
reading a current distribution intensity from a centroid of the base-specific intensity distribution; determining a first current intensity correction parameter and a second current intensity correction parameter for the current sequencing cycle based on the current intensity and the current distribution intensity;
applying a decay factor to the first and second current intensity correction parameters, respectively, to generate a first decayed current intensity correction parameter and a second decayed current intensity correction parameter for the current sequencing cycle; and
determining the first and second accumulated intensity correction parameters by accumulating the first and second decayed current intensity correction parameters and preceding accumulated intensity correction parameters at each of the one or more preceding sequencing cycles.

7. The computer-implemented method of claim 6 , wherein the decay factor is kept fixed for a certain number of sequencing cycles of the sequencing run, and exponentially decayed thereafter based on a decay logic.

8. The computer-implemented method of claim 7 , wherein the decay logic is 1−1/tau, where tau is a predefined number.

9. The computer-implemented method of claim 6 , wherein closed-form expressions for the first and second current intensity correction parameters, and the first and second accumulated intensity correction parameters are determined using a least-squares solution.

10. The computer-implemented method of claim 1 , further including iterating the accessing, the determining, the determining, the correcting, and the base calling for the target cluster at successive sequencing cycles of the sequencing run.

11. The computer-implemented method of claim 1 , further including executing the accessing, the determining, the determining, the correcting, and the base calling in parallel for multiple clusters.

12. A computer-implemented method of base calling a target cluster, the computer-implemented method comprising:
accessing current intensity data and historic intensity data for the target cluster;
wherein the current intensity data is for a current sequencing cycle of a sequencing run, and
wherein the historic intensity data is for one or more preceding sequencing cycles of the sequencing run,

generating, on a cluster-by-cluster basis, a set of coefficients for inter-cluster intensity profile variation correction using the current intensity data and the historic intensity data;
correcting, based on the set of coefficients, next intensity data to generate corrected next intensity data;
wherein the next intensity data is for a next sequencing cycle of the sequencing run; and

base calling the target cluster at the next sequencing cycle based on the corrected next intensity data.

13. The computer-implemented method of claim 12 , further comprising iterating the accessing, the generating, the correcting, and the base calling for the target cluster at successive sequencing cycles of the sequencing run.

14. The computer-implemented method of claim 12 , further comprising executing the accessing, the generating, the correcting, and the base calling in parallel for multiple clusters.

15. The computer-implemented method of claim 12 , wherein the set of coefficients for inter-cluster intensity profile variation correction includes a scale correction coefficient and a shift correction coefficient corresponding to the current sequencing cycle.

16. The computer-implemented method of claim 15 , wherein the shift correction coefficient is subtracted from the next intensity data to generate a shifted next intensity data, and the shifted next intensity data is divided by the scale correction coefficient to generate the corrected next intensity data.

17. The computer-implemented method of claim 16 , wherein the scale correction coefficient and the shift correction coefficient are generated based on a first accumulated intensity correction parameter, wherein the first accumulated intensity correction parameter is an accumulation of distribution intensities measured in a corresponding intensity channel for the target cluster at the current sequencing cycle and at each of the one or more preceding sequencing cycles.

18. The computer-implemented method of claim 17 , wherein each of the distribution intensities at a corresponding sequencing cycle is determined from a centroid of a base-specific intensity distribution to which the target cluster belongs at the corresponding sequencing cycle.

19. The computer-implemented method of claim 15 , wherein the scale correction coefficient and the shift correction coefficient are generated based on a second accumulated intensity correction pa

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

• G06V10/507

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

• G16B40/30

  Unsupervised data analysis · 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