View source for 18391487. CONTEXT-DEPENDENT BASE CALLING simplified abstract (ILLUMINA, INC.)

=CONTEXT-DEPENDENT BASE CALLING=


==Organization Name==

[[:Category:ILLUMINA, INC.|ILLUMINA, INC.]]


[[Category:ILLUMINA, INC.]]

==Inventor(s)==

[[:Category:Gery Vessere of San Francisco CA (US)|Gery Vessere of San Francisco CA (US)]][[Category:Gery Vessere of San Francisco CA (US)]]

[[:Category:David Olmstead Bracher of San Diego CA (US)|David Olmstead Bracher of San Diego CA (US)]][[Category:David Olmstead Bracher of San Diego CA (US)]]

[[:Category:Aathavan Karunakaran of Berkeley CA (US)|Aathavan Karunakaran of Berkeley CA (US)]][[Category:Aathavan Karunakaran of Berkeley CA (US)]]

==CONTEXT-DEPENDENT BASE CALLING - A simplified explanation of the abstract==


This abstract first appeared for US patent application 18391487 titled 'CONTEXT-DEPENDENT BASE CALLING

The technology disclosed in this patent application is focused on context-dependent base calling, involving the use of k-mer-specific centroids to improve accuracy in sequencing.

* Memory stores k-mer-specific centroids for k-mers.
* Centroids are learned by training a base calling pipeline to represent base calls in k-mer-specific time series.
* Predicted centroids are generated by transforming the time series and merging them on a sequencing cycle basis.
* Training loss is determined by comparing predicted intensity values with known intensity values of base calls.
* Updated centroids are stored and used at runtime to base call bases in a sequence based on k-mer context.

Potential Applications:
- Improving accuracy in DNA sequencing.
- Enhancing the efficiency of base calling processes in genomics research.

Problems Solved:
- Addressing inaccuracies in base calling.
- Providing a context-dependent approach to improve sequencing results.

Benefits:
- Increased accuracy in DNA sequencing.
- Enhanced efficiency in genomics research.
- Improved reliability of base calling processes.

Commercial Applications:
Title: Context-Dependent Base Calling Technology in Genomics
This technology could be utilized in research laboratories, biotechnology companies, and medical institutions for DNA sequencing and genomic analysis.

Questions about Context-Dependent Base Calling Technology:
1. How does this technology improve the accuracy of base calling in DNA sequencing?
2. What are the potential implications of using k-mer-specific centroids in genomics research?

Frequently Updated Research:
Stay updated on advancements in DNA sequencing technologies and genomics research to understand the latest trends and developments in context-dependent base calling.


==Original Abstract Submitted==

The technology disclosed is directed to context-dependent base calling. The technology disclosed describes a system including memory storing k-mer-specific centroids for k-mers. The k-mer-specific centroids are learned by training a base calling pipeline to represent base calls of an already base called sequence in k-mer-specific time series, transform the k-mer-specific time series into predicted k-mer-specific centroids, merge the predicted k-mer-specific centroids on a sequencing cycle-by-sequencing cycle basis to generate predicted per-sequencing cycle intensity values, determine a training loss (e.g., a transformation loss) based on comparing the predicted per-sequencing cycle intensity values against known intensity values of the base calls, update the predicted k-mer-specific centroids based on the determined training loss, and store the updated centroids as the k-mer-specific centroids. The system also includes runtime logic that uses the k-mer-specific centroids to base call bases in a yet-to-be base called sequence in dependence upon k-mer context.



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