Genome Sequencing Library Tagging for Mixed-Resolution Coverage
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Solution Overview
Problem
Current next-generation sequencing (NGS) assays lack a universal solution for achieving high coverage and detailed insights across various genomic regions, including coding regions, whole genomes, and transcriptomes, especially for complex mutations and poorly understood genetic diseases.
Innovation Solution
A method involving the tagging of sequencing libraries with sequence identifier tags, allowing for the differentiation and amplification of subsets of libraries, followed by targeted sequencing to achieve varying coverage levels across different genomic regions, including the use of mismatching primers and polymerases with and without proofreading activity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If NGS assays are tailored to targeted markers and analyses, then specific gene analysis precision is improved, but versatility and fit-all solutions are worsened
Solution Approach 1:
The patent implements a universal NGS assay system that can simultaneously perform multiple functions: whole genome sequencing, exome sequencing, and targeted gene panel sequencing using a single assay platform. The system uses a pooled library approach where different sequencing libraries (whole genome, exome, targeted) are combined and sequenced together, allowing one assay to serve multiple analytical purposes and eliminating the need for separate tailored assays for different genomic regions.
2Measurement precision
If high coverage is achieved for specific regions, then detection quality is improved, but sequencing cost and complexity are worsened
Solution Approach 1:
The patent segments the sequencing analysis into different library types (whole genome sequencing library, exome sequencing library, targeted sequencing library) that can be prepared separately and then pooled together for sequencing. This allows high coverage to be achieved for specific regions of interest through targeted enrichment while maintaining the option to sequence the entire genome at lower coverage, thereby optimizing detection quality without uniformly increasing complexity across the entire sequencing process.
Solution Approach 2:
The patent merges multiple sequencing libraries (whole genome, exome, and targeted panels) into a single pooled library that is sequenced together in one NGS run. This combining approach allows the system to achieve high coverage for specific targeted regions while sharing the sequencing cost and computational resources across all library types, thereby reducing overall complexity and cost compared to performing separate high-coverage sequencing for each region.
3Productivity
If multiple sequencing libraries are pooled together, then productivity is improved, but library differentiation and analysis are worsened
Solution Approach 1:
The patent introduces sequence identifier tags as intermediary elements that are incorporated into different sequencing libraries (whole genome, exome, targeted) to enable their differentiation after pooling. These tags act as mediators that allow the sequencing system to distinguish between different library types during the sequencing process, enabling accurate data analysis and assignment while maintaining the productivity benefits of pooled sequencing.
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
Enables the simultaneous high-quality analysis of multiple genes and genomic regions, enhancing the detection of complex mutations and providing detailed genetic information for personalized medicine applications.
Implementation Method 1
amplifying the DNA fragments to obtain the initial library pool
Implementation Method 2
hybridizing the denatured DNA fragments with primers
Implementation Method 3
amplifying the DNA fragments to obtain the initial library pool
Data Source
AI summary
A method for analyzing various regions of a genome at different resolutions, is disclosed herein, wherein the method comprises: producing, a whole-genome sequencing (WGS) library, wherein the WGS library is created from at least one of: DNA, RNA, and TNA; enriching, the WGS library, for each of one or more regions of interest; producing, a final sequencing library, wherein a first grouping of genomic regions are represented at a higher coverage than a second grouping of genomic regions; applying, NGS sequencing, to the final sequencing library, creating genetic data; and analyzing, the genetic data, to identify genetic markers.