Personalized Nucleic Acid Probe Panels for Cost-Effective Variant Testing
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Solution Overview
Problem
The clinical adoption of exome-scale sequencing is limited by high costs, particularly in cancer research where deeper DNA sequencing is required, and existing array-based DNA synthesis methods lack the ability to leverage personalized genetic information for targeted applications.
Innovation Solution
A method for personalized genetic testing involving the synthesis of nucleic acid probe molecules on an array or selection from a collection, tailored to specific genetic variants identified in a subject's nucleic acid sequence data, to perform assays on biological samples and generate data indicative of genetic variant presence or absence.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If exome-scale sequencing is performed using conventional methods, then comprehensive genetic analysis is achieved, but costs become prohibitively high
Solution Approach 1:
The patent extracts and synthesizes only the specific nucleic acid probe molecules corresponding to identified genetic variants, rather than performing comprehensive sequencing of all exonic regions. This targeted extraction approach maintains diagnostic precision for known variants while dramatically reducing costs by eliminating analysis of non-variant regions.
Solution Approach 2:
The method performs preliminary whole exome sequencing to identify genetic variants, then uses this information to design and synthesize a customized panel of nucleic acid probes for targeted re-analysis. This preliminary action enables subsequent cost-effective focused testing on the same or additional samples.
2Productivity
If array-based DNA synthesis is used for high throughput, then productivity increases, but ability to personalize based on individual genetic characteristics is lost
Solution Approach 1:
The patent employs dynamic probe panel design where the set of nucleic acid probes is customized for each patient based on their individually identified genetic variants. The synthesis system adapts its output to match each patient's specific genetic profile while maintaining high throughput through automated array-based synthesis of the personalized probe sets.
Solution Approach 2:
The array synthesis platform serves multiple functions: it can synthesize standardized high-volume probe sets for common variants, and simultaneously generate customized probe panels for individual patients with rare or unique variants. This multi-functionality maintains productivity while enabling personalization.
3Measurement precision
If deeper DNA sequencing is performed for cancer research, then detection sensitivity improves, but costs increase significantly
Solution Approach 1:
The patent applies enhanced sequencing depth and analysis rigor specifically to regions containing identified genetic variants and their surrounding contexts, rather than uniformly applying deep sequencing across the entire genome. This localized quality enhancement maintains detection sensitivity for cancer-relevant variants while reducing overall sequencing costs.
Data Source
AI summary
This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.