STR Allelotyping for NGS Sample Identity Assurance

Resolve Bottlenecks,
Find Innovative SolutionsGenerate Solutions

Solution Overview

Problem

Current Next Generation Sequencing (NGS) processes face challenges in ensuring sample identity, leading to false positive variant detections and genotype misclassification due to sample swap or contamination, which complicates the assurance of correct sample identity throughout genetic analysis.

Innovation Solution

A method combining short tandem repeat (STR) amplification and genetic sequencing to determine allele concordance, using a panel of oligonucleotides and computational workflows to ensure sample identity, with a statistical framework that rules out errors with high probability, thereby confirming whether samples come from the same individual.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If array-based genotyping with SNP microarrays is used to ensure sample identity, then concordance between genotype profiling can be obtained, but the workflow requires 2-3 days to complete and requires initial instrumentation and modifications

Engineering Contradiction:
Improvesample identity assuranceVSAvoidworkflow duration
Core Design Contradiction:
ReliabilityVSLoss of time

Solution Approach 1:

The invention extracts only the essential STR loci from the genome that are sufficient for sample identity verification, rather than using comprehensive SNP microarray panels. This selective extraction of key genetic markers enables rapid STR amplification and sequencing to confirm sample identity within 4-6 hours, eliminating the need for lengthy 2-3 day microarray workflows while maintaining reliability

Inventive Principle:
Principle #2Taking out (Extraction)

Solution Approach 2:

The method performs preliminary STR amplification and allele determination before full NGS analysis. By establishing sample identity through rapid STR genotyping as a preliminary quality control step, the system prevents downstream errors from sample swaps or contamination, enabling early verification without delaying the main sequencing workflow

Inventive Principle:
Principle #10Preliminary action

2Measurement precision

If comprehensive NGS processes are performed, then deep genomic analysis is achieved, but sample swap or contamination may result in false positive variant detections and genotype misclassification

Engineering Contradiction:
Improvegenomic analysis accuracyVSAvoidsample identity verification
Core Design Contradiction:
Measurement precisionVSReliability

Solution Approach 1:

The invention performs preliminary STR amplification and allele determination before full NGS analysis. By establishing sample identity through rapid STR genotyping as a preliminary quality control step, the system prevents downstream errors from sample swaps or contamination, enabling early verification without delaying the main sequencing workflow

Inventive Principle:
Principle #10Preliminary action

Solution Approach 2:

The system implements feedback by comparing STR-derived alleles with NGS-derived alleles for the same loci. This cross-validation provides feedback on sample identity consistency, allowing the system to detect and flag potential sample swaps or contamination events that would compromise NGS results, thereby maintaining measurement precision through continuous verification

Inventive Principle:
Principle #23Feedback

3Reliability

If custom designed array workflow is created to optimize concordance between NGS panel data and SNP microarray data, then concordance is improved, but the workflow complexity and cost increase

Engineering Contradiction:
Improveconcordance between NGS and array dataVSAvoidworkflow complexity
Core Design Contradiction:
ReliabilityVSDevice complexity

Solution Approach 1:

The invention merges STR amplification with NGS panel sequencing into a unified workflow. By designing NGS panels that include STR loci alongside target genes, the system simultaneously achieves sample identity verification and genomic analysis in a single process, eliminating the need for separate custom array workflows and reducing overall complexity

Inventive Principle:
Principle #5Merging (Combining)

Solution Approach 2:

The NGS panel serves multiple functions: it performs target gene sequencing for diagnostic purposes and simultaneously captures STR loci for sample identity verification. This multi-functionality eliminates the need for separate genotyping arrays, reducing device complexity and workflow steps while maintaining high concordance through integrated analysis

Inventive Principle:
Principle #6Universality (Multi-functionality)

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 simplifies the workflow, reduces errors to less than 1 in 1,000,000,000,000, and ensures accurate sample identity within 4-6 hours, making it more efficient and reliable for laboratories, especially those with small sample volumes.

Implementation Method 1

determining a first allelotype for a sample via short tandem repeat (STR) amplification

Methodology Applied
Scientific EffectPCR amplification: Enzyme

Implementation Method 2

determining a second allelotype for the sample via genetic sequencing

Methodology Applied
Scientific EffectGenetic sequencing:

Data Source

PatentUS20200005894A1Method and system for sample identity assurance
Publication Date: 2020.01.02 RADY CHILDRENS HOSPITAL RES CENT

AI summary

The present disclosure provides a method for genetic analysis including allelotyping as well as a system for implementing such analysis.