Custom Nucleic Acid Assays for Personalized Cancer Mutation Tracking

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Solution Overview

Problem

Existing cancer monitoring methods lack personalized and efficient approaches to track genetic mutations and identify disease progression or recurrence, particularly in the context of cancer-driving mutations and therapy resistance.

Innovation Solution

Custom assays are developed using nucleic acid probes tailored to a subject's genetic characteristics, synthesized based on sequencing data from biological samples, to detect genetic variants and generate data indicative of tumor metastasis, second primary cancers, or subclonal mutations, facilitating therapeutic interventions.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If custom assays are developed to track genetic mutations, then measurement precision is improved, but device complexity increases

Engineering Contradiction:

Improvedetection accuracy of genetic variantsVSAvoidassay customization complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent performs preliminary sequencing of a screening biopsy sample to identify patient-specific mutations before developing the custom panel. This advance characterization allows the assay to be tailored to the patient's specific genetic profile, improving detection precision while managing complexity through pre-planned customization.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The custom panel is designed to target specific sequence data corresponding to both subject-specific loci and other loci known for cancer-causing or therapy resistance mutations. This localized focus on relevant genetic regions improves measurement precision by concentrating detection capability on the most critical targets.

Inventive Principle:

Principle #3Local quality

2Adaptability or versatility

If custom panels are designed based on sequencing data, then adaptability is improved, but manufacturing precision requirements increase

Engineering Contradiction:

Improvepatient-specific mutation trackingVSAvoidprobe sequence accuracy

Core Design Contradiction:

Adaptability or versatilityVSManufacturing precision

Solution Approach 1:

The panel design is finalized based on advance sequencing results, allowing precise incorporation of patient-specific mutation information into the probe sequences. This preliminary characterization enables accurate manufacturing of customized probes tailored to individual patient needs.

Inventive Principle:

Principle #10Preliminary action

3Reliability

If multiple biological samples are analyzed at different time points, then reliability is improved, but loss of time increases

Engineering Contradiction:

Improvecancer monitoring accuracyVSAvoidmonitoring duration

Core Design Contradiction:

ReliabilityVSLoss of time

Solution Approach 1:

The custom panel enables continuous monitoring of cancer-related genetic variants across multiple time points, allowing detection of disease progression, recurrence, or response to therapy. This continuous surveillance improves reliability by providing longitudinal data while the modular panel design helps manage time investment through efficient re-use.

Inventive Principle:

Principle #20Continuity of useful action

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

The custom assays provide personalized cancer monitoring by accurately identifying genetic variants, enabling early detection of tumor metastasis, second primary cancers, and subclonal mutations, thereby guiding targeted therapeutic interventions.

Implementation Method 1

using a plurality of genetic characteristics to determine a nucleic acid configuration of an assay, which nucleic acid configuration includes nucleic acid sequences of a plurality of nucleic acid probe molecules, wherein the nucleic acid sequences are selective for genetic variants

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS20250270653A1Customized assays for personalized cancer monitoring

Publication Date: 2025.08.28 PERSONALIS INC

AI summary

The present disclosure provides methods and systems for personalized genetic testing of disease in a subject, in particular for identifying and tracking genetic mutations identified in an individual subject to monitor for cancer or for the spread or recurrence of the disease. In some embodiments, custom assays, including custom panels designed to target sequence data corresponding to both subject-specific loci and other loci known for cancer-causing or therapy resistance mutations, are designed based upon the sequencing of a screening biopsy sample. Such custom assays are then run on subsequently obtained tissue samples, such as tissue obtained from a surgical resection of a primary or metastatic tumor or from a lymph node biopsy. The subsequently obtained tissue samples can be taken from the subject at various time points after an initial screening biopsy to further allow for extended monitoring of the subject for spread or recurrence of the disease.