Regulatory Element Enrichment for Accurate Genomic Biomarker Detection

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Solution Overview

Problem

Current methods for whole genome sequencing to analyze genomic biomarkers are time-consuming and expensive, making early disease diagnosis, prediction, and treatment challenging.

Innovation Solution

A method involving the use of a probe set to enrich nucleic acid samples for regulatory elements, followed by sequencing and computer processing to determine gene expression profiles, allowing for the identification of diseases with high accuracy.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If whole genome sequencing is used to analyze genomic biomarkers, then comprehensive genetic information is obtained, but the process becomes time-consuming and expensive

Engineering Contradiction:

Improvecomprehensive genetic informationVSAvoidtime-consuming

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent extracts and analyzes only the regulatory elements (promoters, enhancers, silencers, insulators) from the genome rather than sequencing the entire genome. This targeted extraction of functional regions provides comprehensive genetic information about gene regulation while significantly reducing sequencing time and cost compared to whole genome sequencing.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The genome is segmented into functional regulatory elements (promoters, enhancers, silencers, insulators) which are then analyzed separately. This segmentation allows focused analysis of disease-relevant regions without the overhead of processing non-coding and redundant genomic sequences, reducing overall analysis time while maintaining diagnostic precision.

Inventive Principle:

Principle #1Segmentation

2Measurement precision

If whole genome sequencing is used to analyze genomic biomarkers, then comprehensive genetic information is obtained, but the cost becomes prohibitively expensive

Engineering Contradiction:

Improvecomprehensive genetic informationVSAvoidcost

Core Design Contradiction:

Measurement precisionVSEase of manufacture

Solution Approach 1:

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent performs partial sequencing focused specifically on regulatory elements rather than complete genome sequencing. This partial action approach captures the essential disease-related genetic information contained in regulatory regions while avoiding the excessive cost of sequencing the entire genome, achieving cost-effectiveness without sacrificing diagnostic accuracy.

Inventive Principle:

Principle #16Partial or excessive action

3Productivity

If targeted enrichment of regulatory elements is performed, then time and cost are reduced, but comprehensive genomic analysis may be limited

Engineering Contradiction:

Improvetime and cost efficiencyVSAvoidcomprehensive genomic analysis

Core Design Contradiction:

ProductivityVSMeasurement precision

Solution Approach 1:

The patent applies local quality by focusing analytical resources on the specific functional regions (regulatory elements) that are most relevant to disease pathology. Rather than uniform whole-genome analysis, the method concentrates sequencing depth and computational resources on promoters, enhancers, silencers, and insulators where disease-causing variants are most likely to occur, achieving both efficiency and diagnostic precision.

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The patent changes the analysis parameters from whole-genome coverage to targeted regulatory element coverage. By adjusting the scope of sequencing to focus on functional regulatory regions and modifying the bioinformatics analysis pipeline to interpret regulatory element variants, the method achieves time and cost efficiency while maintaining comprehensive genomic analysis capability for disease-relevant regions.

Inventive Principle:

Principle #35Parameter changes

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 reduces the time and cost of extracting information from genetic material, enabling accurate disease diagnosis and prediction with an accuracy of at least 90%.

Implementation Method 1

using a probe set comprising probes having sequencing complementarity with a plurality of regulatory elements to enrich the nucleic acid sample for nucleic acid sequences in the nucleic acid sample comprising at least a subset of the regulatory elements

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS20230175058A1Methods and systems for abnormality detection in the patterns of nucleic acids

Publication Date: 2023.06.08 FREENOME HOLDINGS INC

AI summary

Systems, media, methods, and kits disclosed herein can improve analysis capabilities of genomic materials. Results from such analyses can be used to detect genomic biomarkers in one or more genomic materials. The systems, media, methods and kits disclosed herein can identify changes or patterns among samples, and can employ machine learning methods to explore changes or potential changes in biological conditions or risks thereof. Further, the systems, media, methods and kits disclosed herein can utilize machine learning algorithms to analyze samples with high accuracy.