Indel Probe Design for Complex Genetic Variation Detection

Resolve Bottlenecks,
Find Innovative SolutionsGenerate Solutions

Solution Overview

Problem

Current methods lack high-throughput, cost-effective, and accurate means for detecting and distinguishing between insertion/deletion events in genomes, particularly for complex and multi-base indels, which are essential for understanding genetic diseases like cancer and diabetes.

Innovation Solution

The development of computer-implemented methods and systems for designing indel probes that are compatible with existing SNP probe systems, allowing for the detection of a wide range of indels using oligonucleotide probes, including those previously undetectable, by shifting the probe sequence to align interrogation bases correctly.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If existing SNP probe systems are used for indel detection, then system compatibility is maintained, but detection accuracy and recovery rate for complex indels deteriorates

Engineering Contradiction:

Improvesystem compatibilityVSAvoidindel detection accuracy

Core Design Contradiction:

ReliabilityVSMeasurement precision

Solution Approach 1:

The patent modifies probe sequences locally by shifting them to align interrogation bases correctly with indel regions. This local adjustment allows the probe to maintain compatibility with existing SNP probe systems while achieving accurate detection of complex indels that previous methods could not detect

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The patent changes the probe sequence parameters by shifting the probe sequence to align interrogation bases correctly. This parameter modification enables the probe to detect a wide range of indels including complex and multi-base indels while maintaining compatibility with existing SNP probe systems

Inventive Principle:

Principle #35Parameter changes

2Measurement precision

If probe sequences are shifted to align interrogation bases correctly, then indel detection accuracy improves, but probe design complexity increases

Engineering Contradiction:

Improveindel detection accuracyVSAvoidprobe design complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent applies parameter changes by shifting probe sequences to align interrogation bases correctly with indel regions. This systematic approach improves detection accuracy while the computer-implemented methods automate the design process, managing the increased complexity

Inventive Principle:

Principle #35Parameter changes

3Productivity

If computer-implemented methods are used for probe design, then productivity and recovery rate improve, but system complexity increases

Engineering Contradiction:

Improveprobe design efficiencyVSAvoidsystem complexity

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent replaces manual probe design methods with computer-implemented methods and algorithms. This substitution dramatically improves productivity and enables the design of probes for complex indels, while the automated nature of the computer system manages the complexity of the design process

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

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 significantly improves the recovery rate of indel detection, from 75% for single-base indels to 100%, and enables the detection of complex and multi-base indels, enhancing the capability to identify genetic variations associated with diseases.

Implementation Method 1

Nucleic acid probes targeting indels

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS10535420B2Systems and methods for probe design to detect the presence of simple and complex indels

Publication Date: 2020.01.14 AFFYMETRIX INC

AI summary

Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.