Haplotype Visualization Using Barcodes for Structural Variant Analysis
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Solution Overview
Problem
Existing tools do not adequately address the need for visually assessing structural variants such as deletions, duplications, copy-number variants, insertions, inversions, translocations, long terminal repeats (LTRs), and short tandem repeats (STRs) in nucleic acid sequencing data.
Innovation Solution
A system and method for visually assessing structural variants by using barcode information to identify potential breakpoints and obtain phasing information, utilizing a network-connected computing system with microprocessors, persistent and non-persistent memory, and visualization tools to display structural variation and phasing information on a remote client computer.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If existing visualization tools (Consed, EagleView, HapEdit) are used, then basic sequencing data visualization is achieved, but structural variant assessment capability is insufficient
Solution Approach 1:
The visualization tool is designed to perform multiple functions: displaying sequence reads, visualizing barcodes, identifying structural variants, and providing phasing information within a single integrated platform. This multi-functionality resolves the contradiction by making the tool adaptable to various genomic analysis needs while fully utilizing barcode information for structural variant detection.
Solution Approach 2:
The tool segments the visualization into distinct functional components: sequence read display, barcode visualization, structural variant identification, and phasing information presentation. This segmentation allows each component to be optimized for its specific purpose while working together to provide comprehensive structural variant assessment capability.
2Measurement precision
If barcode information is used to identify structural variants, then detection precision is improved, but computational complexity increases
Solution Approach 1:
Barcode information is processed and organized in advance to create a structured representation that facilitates efficient structural variant detection. By pre-processing the barcode data to identify patterns and relationships, the system achieves high detection precision without requiring excessive computational complexity during the actual variant calling process.
3Measurement precision
If phasing information is obtained through barcode analysis, then haplotype assembly accuracy is improved, but data processing time increases
Solution Approach 1:
The system creates simplified representations or models of the barcode data that capture the essential phasing information. By working with these copied representations rather than the raw barcode data, the system achieves accurate haplotype assembly while reducing the computational time required for data processing.
Data Source
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AI summary
A system for providing structural variation or phasing information is provided. The system accesses a nucleic acid sequence dataset corresponding to a target nucleic acid in a sample. The dataset comprises a header, synopsis, and data section. The data section comprises a plurality of sequencing reads. Each sequencing read comprises a first portion corresponding to a subset of the target nucleic acid and a second portion that encodes an identifier for the sequencing read from a plurality of identifiers. One or more programs in the memory of the system use a microprocessor of the system to provide a haplotype visualization tool that receives a request for structural variation or phasing information from the dataset. The request is evaluated against the synopsis thereby identifying portions of the data section. Structural variation or phasing information is formatted for display in the haplotype visualization tool using the identified portions of the data section.