Competitive Template Nucleic Acid Quantification

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Solution Overview

Problem

Current methods for multi-gene expression measurement lack effective quality control, particularly for regulatory compliance, and struggle to accurately quantify low levels of nucleic acids, leading to issues with false negatives and positives.

Innovation Solution

A method involving the amplification and comparison of nucleic acids using competitive templates, with techniques such as microfluidic capillary electrophoresis, oligonucleotide arrays, or mass spectrometry, to achieve precise enumeration and reduce variability, allowing for the detection of small differences and variations in nucleic acid levels.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If conventional multi-gene expression measurement methods are used, then gene expression can be measured, but quality control is ineffective and regulatory compliance cannot be met

Engineering Contradiction:

Improvequality control effectivenessVSAvoidmeasurement system complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent introduces competitive templates as intermediary molecules that compete with target nucleic acids for amplification. These templates contain known concentrations and serve as internal controls, enabling accurate quantification and quality assessment without requiring complex external calibration systems.

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The patent transforms qualitative gene expression data into quantitative measurements by changing the measurement parameter from presence/absence to precise molecular counting. This is achieved through competitive amplification where the ratio of target to competitive template products provides accurate quantification of low-abundance nucleic acids.

Inventive Principle:

Principle #35Parameter changes

2Measurement precision

If conventional methods are used to measure low levels of nucleic acids, then measurement is attempted, but accuracy deteriorates due to false negatives and positives

Engineering Contradiction:

Improvenucleic acid quantification accuracyVSAvoidfalse negative and positive rates

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

The patent implements feedback through competitive templates that provide real-time information about amplification efficiency and reaction conditions. By comparing the amplification of target nucleic acids against competitive templates with known concentrations, the system self-corrects for variations and accurately quantifies low-abundance targets, reducing false results.

Inventive Principle:

Principle #23Feedback

3Measurement precision

If competitive templates with known concentrations are used, then accurate enumeration of low-level nucleic acids is achieved, but the system complexity increases

Engineering Contradiction:

Improvenucleic acid enumeration accuracyVSAvoidcompetitive template system complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent designs competitive templates that serve multiple functions simultaneously: they compete for amplification, provide internal controls, enable quantification, and allow quality assessment. This multi-functionality reduces the need for separate control experiments and simplifies the overall measurement system despite the added molecular complexity.

Inventive Principle:

Principle #6Universality (Multi-functionality)

4Productivity

If conventional amplification methods are used, then nucleic acid amplification occurs, but variability in amplification efficiency leads to poor reproducibility

Engineering Contradiction:

Improveamplification efficiencyVSAvoidamplification reproducibility

Core Design Contradiction:

ProductivityVSStability of the object's composition

Solution Approach 1:

The competitive templates provide feedback on amplification efficiency by competing with target nucleic acids under identical conditions. Any variations in amplification efficiency affect both target and competitive template equally, allowing the system to detect and correct for these variations through ratio-based quantification, thereby improving reproducibility.

Inventive Principle:

Principle #23Feedback

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

This approach enables accurate measurement of low levels of nucleic acids, reduces false positives and negatives, and provides a high degree of precision and reliability, facilitating compliance with regulatory guidelines and improving diagnostic and drug development processes.

Implementation Method 1

combining said first sample with said standardized mixture; co-amplifying said first nucleic acid and said competitive template for said first nucleic acid

Methodology Applied

Scientific EffectCompetition:

Implementation Method 2

amplifying said first nucleic acid

Methodology Applied

Scientific EffectAmplification:

Data Source

PatentUS7527930B2Compositions and methods of use of standardized mixtures for determining an amount of a nucleic acid

Publication Date: 2009.05.05 GENE EXPRESS

AI summary

The present invention is directed to methods and compositions for evaluating nucleic acids, methods of preparing such compositions, and applications and business methods employing such compositions and methods. In particular, the present invention provides business methods for operating a gene expression measurement service.