Nucleic Acid Adaptor Barcodes for Sequencing Error Correction

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Solution Overview

Problem

Next-generation sequencing (NGS) methods face inefficiencies and inaccuracies due to the need for separate steps to purify targeted genomic regions, leading to waste and reduced reliability, and errors in consensus sequence construction.

Innovation Solution

The method involves ligating adaptors with molecular barcodes to nucleic acid duplexes, amplifying, and differentially amplifying primer extension products to enhance sequencing specificity and control, allowing for error correction and targeted sequencing.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If separate purification steps are used to isolate targeted genomic regions, then sequencing specificity is improved, but process time and complexity increase

Engineering Contradiction:

Improvesequencing specificityVSAvoidprocess time

Core Design Contradiction:

ReliabilityVSLoss of time

Solution Approach 1:

The patent combines the purification and sequencing preparation steps into a single integrated process. Adaptors containing molecular barcodes are ligated directly to fragmented nucleic acids, and targeted regions are enriched through hybridization capture in the same reaction mixture, eliminating the need for separate purification steps while maintaining sequencing specificity

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The adaptor molecules serve multiple functions simultaneously: they provide sequencing priming sites, contain molecular barcodes for sample identification, and enable targeted enrichment through hybridization. This multi-functionality consolidates what would otherwise require separate steps into a unified process

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Measurement precision

If molecular barcodes are incorporated into adaptors, then sample identification accuracy is improved, but adaptor design complexity increases

Engineering Contradiction:

Improvesample identification accuracyVSAvoidadaptor design complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The adaptor is divided into distinct functional segments: a hybridization region for target capture, a molecular barcode region for sample identification, and sequencing priming sites. This segmentation allows each component to be optimized independently while maintaining overall simplicity

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The molecular barcode acts as an intermediary element that connects the hybridization region to the sequencing priming sites. This intermediary structure enables sample identification without interfering with the hybridization or sequencing processes, maintaining design simplicity while improving identification accuracy

Inventive Principle:

Principle #24Intermediary (Mediator)

3Productivity

If targeted enrichment is performed during library preparation, then sequencing efficiency is improved, but error rate in consensus sequence increases

Engineering Contradiction:

Improvesequencing efficiencyVSAvoidconsensus sequence accuracy

Core Design Contradiction:

ProductivityVSReliability

Solution Approach 1:

The molecular barcodes provide feedback information that allows for error detection and correction during consensus sequence construction. By tracking the origin of each read through its barcode, the system can identify and correct errors that arise during amplification or sequencing, maintaining high consensus sequence accuracy despite targeted enrichment

Inventive Principle:

Principle #23Feedback

4Quantity of substance

If all genomic regions are sequenced with equal probability, then comprehensive coverage is improved, but data quality for specific targets decreases

Engineering Contradiction:

Improvegenomic coverageVSAvoidtarget sequence accuracy

Core Design Contradiction:

Quantity of substanceVSMeasurement precision

Solution Approach 1:

The patent applies local quality by concentrating sequencing depth on specific target regions through hybridization capture. The adaptors and probes are designed to selectively bind to target sequences, ensuring that sufficient reads are obtained for accurate consensus sequence construction in regions of interest, while still maintaining broad genomic coverage

Inventive Principle:

Principle #3Local quality

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 improves sequencing efficiency by controlling the sequencing start position, reducing complexity, and enhancing data quality through error correction, thereby increasing the reliability of NGS results.

Implementation Method 1

hybridizing and extending a primer that includes: (i) a probe sequence that is complementary to a portion of the target nucleic acid sequence

Methodology Applied

Scientific EffectHybridization:

Implementation Method 2

extending a primer that includes: (i) a probe sequence that is complementary to a portion of the target nucleic acid sequence

Methodology Applied

Scientific EffectDNA synthesis:

Data Source

PatentUS20220333188A1Methods and compositions for enrichment of target polynucleotides

Publication Date: 2022.10.20 MYRIAD WOMENS HEALTH INC

AI summary

High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduce sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.