Systems and methods for identifying somatic structural variants

The method of extracting and grouping soft-clipped reads with k-mer matching in sequencing data effectively addresses the challenge of identifying somatic structural variants, enhancing diagnostic and treatment capabilities for diseases like cancer.

WO2026044179A1 Publication Date: 2026-02-26ROCHE SEQUENCING SOLUTIONS INC
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Patent Information

Application Number
PCT/US2025/043101
Authority / Receiving Office
WO · WO
Patent Type
Applications
Current Assignee / Owner
Priority Date
2024-08-23
Filing Date
2025-08-22
Publication Date
2026-02-26

AI Technical Summary

Technical Problem

Existing systems face challenges in accurately identifying somatic structural variants in sequencing data due to computational intensity and error-prone processes, particularly in sequencing by expansion (SBX) data, which lacks discordant reads and may not provide sufficient data for somatic structural variant detection.

Method used

A method involving soft-clipped read extraction, grouping by breakpoints, and k-mer matching is employed to identify somatic structural variants, utilizing sequencing data from processes like targeted, whole genome, or whole transcriptome sequencing, with error correction and secondary alignment information to enhance accuracy.

Benefits of technology

This approach improves the identification of somatic structural variants, particularly those associated with cancer, by reducing errors and enhancing computational efficiency, enabling better diagnosis, prognosis, and treatment strategies.

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Abstract

Some embodiments relate to methods, systems, uses, or software for identification of structural variants (SVs) for regions of deoxynucleic acid (DNA) sequences. A device may receive, at a processor, a dataset comprising base pair data output from a sequencing by expansion process. A device may extract, at the processor, soft-clipped reads from the received dataset. A device may group, at the processor, the extracted soft-clipped reads based at least on their respective breakpoint. A device may determine, at the processor, a presence or an absence of a somatic structural variant by k-mer matching the grouped and extracted soft-clipped reads. A device may provide, at the processor, at least one determined somatic structural variant responsive to determining the presence of the somatic structural variant
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