Longitudinal Genetic Variant Tracking for Tumor Classification
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Solution Overview
Problem
Current methods for tumor classification are inadequate due to their inability to capture genetic heterogeneity, leading to challenges in predicting treatment response and progression, as they often rely on single locus tests that fail to account for the complex lineage of genomic alterations in cancer.
Innovation Solution
The development of methods to create a tumor classification signature by longitudinally tracking genetic variants in patients, using mutation signatures and telomere integrity scores from nucleic acid samples, which can be compared to databases of known health statuses to guide treatment decisions and predict treatment efficacy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If single locus tests are used for tumor classification, then the test simplicity is maintained, but the ability to capture genetic heterogeneity deteriorates
Solution Approach 1:
The patent segments the tumor genetic analysis into multiple independent locus tests rather than relying on a single test. By analyzing multiple genetic loci simultaneously, the system captures the heterogeneity of tumor genetics while maintaining the simplicity of individual locus-based testing approaches.
Solution Approach 2:
The patent creates a multi-locus testing system that serves multiple functions: it can detect various types of genetic alterations (mutations, copy number variations, structural variants) across different tumor types and stages. This universal approach replaces the need for multiple separate single-locus tests.
2Measurement precision
If longitudinal tracking of multiple genetic variants is implemented, then the detection precision of minimal residual disease is improved, but the device complexity increases
Solution Approach 1:
The patent adds the time dimension to genetic testing by performing longitudinal tracking of multiple genetic variants. Instead of a single cross-sectional analysis, the system collects and compares genetic data at multiple time points, enabling detection of minimal residual disease through temporal changes in variant frequencies.
Solution Approach 2:
The patent uses digital copying of genetic information through next-generation sequencing to track multiple variants simultaneously. By creating and analyzing digital copies of tumor DNA at different time points, the system achieves high detection precision without requiring complex physical manipulation of biological samples.
3Measurement precision
If comprehensive genetic variation sampling is performed through time, then the tumor classification accuracy is improved, but the loss of time for analysis increases
Solution Approach 1:
The patent performs preliminary sampling and storage of genetic variants at multiple time points during treatment. By collecting and preserving genetic information in advance, the system enables rapid retrospective analysis and comparison, reducing the time required for comprehensive classification when results are needed.
Solution Approach 2:
The patent replaces time-consuming manual analysis methods with automated computational approaches. Next-generation sequencing and bioinformatics algorithms efficiently process and analyze comprehensive genetic variation data, reducing analysis time while maintaining or improving classification accuracy.
Data Source
AI summary
Aspects of the invention relate to methods for tracking patient health by longitudinally tracking genetic variants in patients, such that it is possible to provide a tumor, or mutation, classification signature. Longitudinal tracking improves the ability to detect minimal residual disease (MRD; the small number of cells that remain in the patient after treatment and/or during remission) and/or treatment response at an early stage, both of which can help guide treatment decisions and guard against missing different intra-/inter-tumor responses in a patient.