Pre-Operative Bodily Fluid Sequencing for Tumor Genome Reference
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Solution Overview
Problem
Existing cancer diagnostics face challenges in early detection and monitoring due to the low sensitivity of conventional methods, limited availability of tumor tissue samples, and the inability to accurately assess metastatic potential, leading to difficulties in timely therapeutic decision-making.
Innovation Solution
Utilizing pre-operative bodily fluids such as blood, urine, saliva, and surgical lavage fluids to create a tumor-informed reference library by sequencing nucleic acids, allowing for the detection of genomic variants and monitoring therapeutic efficacy, minimal residual disease, and metastasis through methods like sequencing, PCR, and machine learning algorithms.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional cfDNA extraction kits are used, then the method is simple and accessible, but the sensitivity is low and early cancer detection is difficult
Solution Approach 1:
The patent performs preliminary sequencing of the tumor-informed reference library before the diagnostic assay. By pre-characterizing the tumor genome from surgical lavage fluid or other pre-operative samples, the system establishes a baseline for detecting minimal residual disease and monitoring therapy response, thereby improving detection sensitivity without requiring complex real-time sequencing during diagnosis
Solution Approach 2:
The patent creates a molecular copy of the tumor genome by sequencing cfDNA from surgical lavage fluid or other bodily fluids to generate a tumor-informed reference library. This digital copy serves as a template for detecting tumor DNA in subsequent samples, enabling high-sensitivity detection without needing to repeatedly perform complex sequencing procedures
2Loss of information
If tissue biopsy is used, then the sample is informative for diagnosis, but the sample availability is limited and invasive procedures are required
Solution Approach 1:
The patent uses surgical lavage fluid or other pre-operative bodily fluids as an intermediary medium to access tumor DNA without requiring direct tissue biopsy. The lavage fluid serves as a bridge that contains tumor-derived cfDNA, enabling non-invasive or minimally invasive sampling while still providing comprehensive tumor genomic information for diagnosis and prognosis
Solution Approach 2:
The patent creates a molecular copy of the tumor genome by sequencing cfDNA from surgical lavage fluid or other bodily fluids to generate a tumor-informed reference library. This digital copy serves as a template for detecting tumor DNA in subsequent samples, enabling high-sensitivity detection without needing to repeatedly perform complex sequencing procedures
3Ease of operation
If pre-operative bodily fluid is used, then the sample is easily accessible and comprehensive tumor information is obtained, but the timing for detection must be optimized
Solution Approach 1:
The patent performs preliminary sequencing of the tumor-informed reference library before the diagnostic assay. By pre-characterizing the tumor genome from surgical lavage fluid or other pre-operative samples, the system establishes a baseline for detecting minimal residual disease and monitoring therapy response, thereby improving detection sensitivity without requiring complex real-time sequencing during diagnosis
Solution Approach 2:
The patent implements a feedback mechanism where the tumor-informed reference library is continuously updated with new genomic data from longitudinal sampling. This allows the system to adapt to tumor evolution over time and maintain optimal detection accuracy throughout the patient's treatment journey, addressing timing concerns through dynamic updating rather than fixed pre-operative sequencing
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
Provides enhanced accuracy in diagnosing and monitoring cancer progression, enabling precise therapeutic selection and personalized surveillance by capturing tumor heterogeneity not represented in traditional biopsy samples.
Implementation Method 1
sequencing nucleic acid from a body fluid sample to obtain a tumor-informed reference library that includes at least one genomic variant specific to a tumor
Implementation Method 2
amplifying extracted cfDNA using quantitative methods, such as qPCR
Data Source
AI summary
The present invention provides methods for using pre-operative bodily fluid as a source for a tumor reference genome. In some embodiments, the pre-operative bodily fluid is sequenced to identify a genomic variant specific to a tumor. In some embodiments, assays are performed to detect the presence of the genomic variant specific to a tumor identified in the pre-operative bodily fluid in surgical drain fluid. In some embodiments, the bodily fluids may be blood, urine, serum, plasma, saliva, sweat, milk, mucous, semen, vaginal or urethral secretions, cerebrospinal fluid, or surgical lavage fluid.