Index Compatibility Validation for Sequencing Pools

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Solution Overview

Problem

Incompatibilities between sequencing devices, indices, and library preparation kits lead to inefficiencies, resource waste, and costly delays in sequencing runs, especially in clinical settings where sample uniqueness complicates obtaining additional samples.

Innovation Solution

A system and method for determining the validity of indexes attached to a pool of samples by analyzing genetic sequence data to ensure compatibility, suggesting index substitutions if necessary, and optimizing sequencing runs using a user application, library preparation system, and cloud-based servers.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If users manually verify compatibility of pooling strategies, indices, and sequencing devices, then sequencing accuracy may be maintained, but time consumption and operational complexity increase significantly

Engineering Contradiction:

Improvesequencing accuracyVSAvoidtime consumption

Core Design Contradiction:

ReliabilityVSLoss of time

Solution Approach 1:

The system performs automatic compatibility verification of indices, pooling strategies, and sequencing devices without requiring manual user intervention. The processor automatically analyzes genetic sequence data, identifies incompatibilities, and suggests corrections, enabling the system to self-validate configurations and eliminate time-consuming manual verification steps while maintaining sequencing accuracy

Inventive Principle:

Principle #25Self-service

Solution Approach 2:

The system provides automated feedback to users regarding compatibility issues detected in sequencing configurations. When incompatibilities are identified, the system communicates specific problems and suggests corrective actions, enabling users to quickly adjust configurations without extensive manual analysis, thus reducing time consumption while ensuring sequencing reliability

Inventive Principle:

Principle #23Feedback

2Reliability

If sequencing runs are repeated due to incompatibilities, then accurate results may be obtained, but resource waste and costs increase

Engineering Contradiction:

Improvesequencing result accuracyVSAvoidresource waste

Core Design Contradiction:

ReliabilityVSLoss of energy

Solution Approach 1:

The system performs compatibility verification before sequencing runs are executed. By analyzing genetic sequence data and identifying potential incompatibilities in advance, the system prevents failed sequencing runs, eliminating the need for repetitive sequencing and associated resource waste while ensuring accurate results are obtained on the first attempt

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The system proactively identifies and flags compatibility issues before they cause sequencing failures. By detecting index conflicts, pooling strategy errors, or device incompatibilities in advance and suggesting corrections, the system prevents harmful sequencing outcomes, avoiding the need for repeat runs and reducing resource consumption

Inventive Principle:

Principle #9Preliminary anti-action

3Productivity

If unique samples are sequenced without validation, then sample throughput may be maximized, but cross-contamination risk increases

Engineering Contradiction:

Improvesample throughputVSAvoidcross-contamination risk

Core Design Contradiction:

ProductivityVSObject-affected harmful factors

Solution Approach 1:

The system automatically validates indices and pooling strategies for unique samples without requiring manual verification. The processor analyzes genetic sequence data to ensure proper sample identification and prevent cross-contamination, enabling high-throughput processing of unique samples while maintaining sample integrity through automated validation mechanisms

Inventive Principle:

Principle #25Self-service

Solution Approach 2:

The system uses computational validation as a low-cost, rapid method to ensure sample integrity. By performing automated compatibility checks and index validation through software analysis rather than expensive or time-consuming physical verification methods, the system enables high throughput of unique samples while maintaining protection against cross-contamination

Inventive Principle:

Principle #27Cheap short-living objects (Disposable)

4Reliability

If manual index verification is performed, then compatibility issues may be detected, but device complexity and operational difficulty increase

Engineering Contradiction:

Improvecompatibility verificationVSAvoidsystem complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The system performs automatic compatibility verification of indices, pooling strategies, and sequencing device configurations without requiring complex manual procedures. The processor automatically analyzes genetic sequence data, identifies incompatibilities, and suggests corrections, simplifying the operational process while maintaining reliable compatibility verification and reducing the need for complex manual validation protocols

Inventive Principle:

Principle #25Self-service

Data Source

PatentUS20250210136A1Systems and Methods for Determining Validity of Indexes Attached to a Pool of Samples

Publication Date: 2025.06.26 ILLUMINA INC

AI summary

Systems and methods are described for determining the validity of indexes attached to a pool of samples. A computing device receives genetic sequence data for each of a plurality of indices to be attached to a plurality of samples in a pool of samples. The computing device analyzes the genetic sequence data for each of the plurality of indices in the pool to determine whether the plurality of indices are compatible with each other. Then in response to determining that the plurality of indices are not compatible with each other, the computing device provides instructions to a user to replace at least one of the plurality of indices with a different index.