Haplotype Visualization for Barcode-Based Structural Variant Phasing
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Solution Overview
Problem
Existing visualization 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 using barcode information to identify potential breakpoints and obtain phasing information, comprising a microprocessor-based haplotype visualization tool that formats and displays structural variation or phasing information over a network connection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If existing visualization tools are used, then basic sequencing data can be viewed, but structural variants cannot be adequately visualized or assessed
Solution Approach 1:
The patent segments the visualization of structural variants into distinct functional modules: barcode information processing, breakpoint identification, phasing information extraction, and visualization display. Each module handles specific aspects of structural variant analysis, enabling comprehensive assessment while maintaining system organization and adaptability.
2Measurement precision
If barcode information is processed to identify breakpoints and phasing, then structural variant detection is improved, but computational complexity increases
Solution Approach 1:
The patent performs preliminary processing of barcode information to pre-identify potential breakpoints and phasing patterns before full structural variant analysis. This preliminary action organizes the data in advance, reducing the computational burden during the main analysis phase while maintaining high identification accuracy.
Solution Approach 2:
The patent introduces an intermediary processing layer that translates raw barcode information into structured breakpoint and phasing data. This intermediary layer simplifies the complexity by creating an intermediate representation that is easier to process and visualize, bridging the gap between raw data and final analysis results.
3Loss of information
If haplotype assembly is performed to disentangle reads, then phasing information is obtained, but computational time increases due to NP-hard nature
Solution Approach 1:
The patent extracts phasing information directly from barcode data without performing complete haplotype assembly. By taking out only the essential phasing signals from the barcode information, the system obtains sufficient phasing data to visualize structural variants without incurring the full computational cost of NP-hard haplotype assembly.
Solution Approach 2:
The patent applies partial action by performing limited haplotype assembly only in regions where structural variants are detected, rather than assembling entire genomes. This selective approach reduces computational time significantly while still obtaining complete phasing information where needed for structural variant analysis.
Data Source
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.