Cancer Biomarker Identification via Functional Polymorphism Segmentation

Solution Overview

Problem

Current methods for assessing the correlation between DNA sequence variations and risk for conditions like bronchogenic carcinoma and COPD are limited by focusing on single polymorphisms, often empirically selected, and require large study populations, making them impractical for identifying effective biomarkers for early detection and treatment.

Innovation Solution

A method involving the comparison of nucleic acid sequences from specific regions of genes such as CEBPG and other genes like XRCC1, ERCC5, SOD1, and GSTP1 to identify nucleotide differences that indicate cancer or lung-related conditions, using samples from subjects to determine biomarkers and polymorphisms associated with these conditions.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Device complexity

If single polymorphism assessment is used, then study complexity is reduced, but measurement precision and reliability of risk assessment deteriorate

Engineering Contradiction:

Improvestudy complexityVSAvoidrisk assessment precision

Core Design Contradiction:

Device complexityVSMeasurement precision

Solution Approach 1:

The patent segments the assessment into two distinct parts: (1) functional identification of polymorphisms affecting gene expression or protein function, and (2) statistical assessment of risk using a manageable number of identified polymorphisms. This segmentation allows functional precision without requiring large-scale statistical studies of all possible polymorphisms.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent performs preliminary functional analysis to identify which polymorphisms have actual biological effects on gene expression or protein function before conducting risk assessment studies. This preliminary filtering step reduces the number of polymorphisms that need to be statistically evaluated, improving both precision and feasibility.

Inventive Principle:

Principle #10Preliminary action

2Reliability

If large study populations are used, then statistical validity of polymorphism assessment is improved, but productivity and practical feasibility deteriorate

Engineering Contradiction:

Improvestatistical validityVSAvoidresearch feasibility

Core Design Contradiction:

ReliabilityVSProductivity

Solution Approach 1:

The patent performs preliminary functional analysis to identify which polymorphisms have actual biological effects on gene expression or protein function before conducting risk assessment studies. This preliminary filtering step reduces the number of polymorphisms that need to be statistically evaluated, improving both precision and feasibility.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent extracts and focuses only on polymorphisms with demonstrated functional consequences (affecting gene expression or protein function) from the vast pool of all possible polymorphisms. This extraction of functionally relevant variants allows statistical assessment with smaller, more practical study populations.

Inventive Principle:

Principle #2Taking out (Extraction)

3Ease of manufacture

If empirically selected polymorphisms are studied, then selection process is simplified, but measurement precision and biological relevance deteriorate

Engineering Contradiction:

Improvepolymorphism selection easeVSAvoidbiomarker accuracy

Core Design Contradiction:

Ease of manufactureVSMeasurement precision

Solution Approach 1:

The patent performs preliminary functional analysis to identify which polymorphisms have actual biological effects on gene expression or protein function before conducting risk assessment studies. This preliminary filtering step reduces the number of polymorphisms that need to be statistically evaluated, improving both precision and feasibility.

Inventive Principle:

Principle #10Preliminary action

Data Source

PatentUS8771947B2Cancer risk biomarkers

Publication Date: 2014.07.08 UNIVERSITY OF TOLEDO

AI summary

The present invention relates to methods and compositions for identifying biomarkers that indicate a biological state, in particular cancer or predisposition to cancer.