Targeted Nanopore Sequencing for Rapid Cancer Classification
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Solution Overview
Problem
Conventional sequencing setups for cancer diagnostics, particularly in neuro-oncology, require significant investment and delay turnaround time, and off-the-shelf products do not cover relevant genes, necessitating custom assays that are inefficient for labs with low specimen numbers.
Innovation Solution
A computer-implemented method using targeted nanopore sequencing and a classification algorithm that selectively sequences specific gene sites, allowing immediate analysis of single samples, such as frozen sections or liquid biopsies, by analyzing initial nucleotide sequences to determine biological states and classify cancer types.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional sequencing setups are used for complete molecular profiling, then comprehensive cancer characterization is achieved, but considerable investment and delayed turnaround time are required
Solution Approach 1:
The patent extracts and sequences only the specific gene sites relevant to neuro-oncology classification rather than performing complete molecular profiling. This targeted approach isolates the essential diagnostic information from the comprehensive but time-consuming full sequencing process, achieving rapid turnaround while maintaining diagnostic accuracy for CNS tumors
Solution Approach 2:
The patent segments the genome into specific target gene sites relevant to cancer classification and sequences only those regions. This segmentation allows the system to focus computational and sequencing resources on diagnostically critical regions, reducing overall sequencing time while preserving measurement precision for cancer characterization
2Ease of operation
If off-the-shelf sequencing products are used, then ease of operation is improved, but relevant genes for neuro-oncology are not covered
Solution Approach 1:
The patent creates a sequencing panel that serves multiple diagnostic functions simultaneously - it covers mutations, fusions, and copy-number variations across multiple neuro-oncology relevant genes in a single assay. This multi-functional panel replaces the need for multiple separate off-the-shelf products while maintaining ease of operation
Solution Approach 2:
The patent implements a dynamic and flexible gene panel that can be adapted to cover different neuro-oncology relevant genes based on specific diagnostic needs. The panel design allows for customization of target genes while maintaining a standardized sequencing workflow, thus preserving ease of operation while achieving adaptability to different clinical scenarios
3Adaptability or versatility
If custom assays are set up for NGS, then gene coverage for neuro-oncology is improved, but efficiency is reduced for labs with low specimen numbers
Solution Approach 1:
The patent applies partial action by sequencing only the essential neuro-oncology relevant genes rather than the entire genome or large panels. This partial sequencing approach reduces the amount of data processing and analysis required per sample, making the assay efficient even when run on single samples or low specimen numbers, while still achieving comprehensive coverage of diagnostically critical genes
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables flexible, efficient, and rapid cancer classification with reduced turnaround time, utilizing nanopore sequencing to enrich target gene sites without needing raw signal conversion, and providing real-time results at lower costs.
Implementation Method 1
selectively sequencing polymers of a biological sample according to at least one target gene site by translocating the polymers through nanopores of a nanopore sequencing system
Data Source
AI summary
The present disclosure relates to a computer-implemented method for cancer diagnosis, comprising: a) selectively sequencing polymers of a biological sample according to at least one target gene site by translocating the polymers through nanopores of a nanopore sequencing system, including: (i) analyzing an initial nucleotide sequence of a first polymer of the biological sample while the first polymer is translocating through a nanopore of the nanopore sequencing system to determine whether the initial nucleotide sequence corresponds to the at least one target gene site; and (ii) continuing the sequencing of the first polymer to obtain measurement data of the first polymer only if the initial nucleotide sequence of the first polymer corresponds to the at least one target gene site: b) determining, based on the measurement data, a biological state of a nucleotide sequence of the first polymer corresponding to the at least one target gene site; and c) classifying a cancer using a classification algorithm based on the biological state of the nucleotide sequence of the first polymer, wherein the classification algorithm is trained based on the at least one target gene site and biological state data pertaining to cancer types.