Sequencing Workflow for Multi-Omics Analysis From One Blood Sample
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Solution Overview
Problem
Existing methods struggle to obtain comprehensive information from a single low-volume biological sample, such as cell-free DNA, without requiring multiple workflows or additional sample material, especially for features like DNA sequences, epigenetic modifications, RNA sequences, nucleosome structure, and plasma proteins.
Innovation Solution
A combined workflow method using proximity extension assays to generate protein-barcoded dsDNA template molecules, incorporating protein-specific and epigenetic markers, and sequencing these molecules to derive multiple types of information, including histone modifications and nucleic acid sequences, from a single sample.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If multiple separate workflows are used to analyze different features (DNA sequence, methylation, RNA, proteins) from a biological sample, then each feature can be analyzed with dedicated methods, but the sample volume required increases and the amount of information obtained per unit sample decreases
Solution Approach 1:
The patent combines multiple analytical workflows (protein analysis via proximity extension assay, DNA sequencing, RNA sequencing, epigenetic modification detection) into a single integrated workflow. All these analyses are performed on the same biological sample without requiring separate sample preparations, thereby maximizing information extraction from limited sample material and eliminating the need for multiple separate workflows that would consume additional sample volume.
Solution Approach 2:
The patent creates a universal analytical platform that can simultaneously perform multiple functions: detecting plasma proteins, analyzing DNA sequences, detecting RNA sequences, and identifying epigenetic modifications. This multi-functional approach allows a single biological sample to be analyzed for diverse molecular features using a unified methodology, thereby reducing total sample consumption while maximizing information yield.
2Productivity
If separate workflows are used for each analysis type, then each analysis can be optimized for its specific purpose, but the complexity of the overall analytical process increases and processing time extends
Solution Approach 1:
The patent merges multiple analytical workflows into a single integrated process where protein analysis, DNA sequencing, RNA sequencing, and epigenetic detection are performed sequentially on the same sample. This consolidation reduces the number of separate sample preparations and processing steps, thereby improving overall productivity and reducing total analysis time despite the inherent complexity of performing multiple analysis types.
3Adaptability or versatility
If traditional protein analysis methods are used, then protein detection can be achieved, but the information cannot be easily integrated with sequencing workflows and sample material is consumed inefficiently
Solution Approach 1:
The patent uses proximity extension assay technology as an intermediary approach that bridges protein analysis and sequencing workflows. The assay generates DNA-based output (barcoded DNA molecules) from protein detection, which can then be directly integrated into standard sequencing library preparation pipelines. This intermediary mechanism enables seamless integration of protein analysis with DNA/RNA sequencing workflows while maintaining sample efficiency.
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 simultaneous analysis of protein analytes, histone modifications, and nucleic acid sequences, enhancing compatibility with existing sequencing techniques and providing a comprehensive data set without diluting or dissociating non-sequence information.
Implementation Method 1
generating a double-stranded DNA segment between the probes of each probe pair in the presence of the corresponding protein analyte
Implementation Method 2
incorporating into the double-stranded DNA segments a protein-specific nucleic acid sequence that serves as a protein identifier barcode
Implementation Method 3
amplifying and sequencing the protein-barcoded dsDNA template molecules; identifying the protein analytes in the biological sample from the protein identifier barcodes observed in the sequence reads generated
Data Source
AI summary
The invention provides a method for the analysis of a biological sample to determine multiple types of information therefrom in a streamlined, combined workflow, where all information is obtained in a sequencing-based analysis. The information includes the presence and concentration of specific plasma proteins in a blood sample: the number, location, and types of histone modifications associated with cell-free DNA obtained from the same sample: the sequence of cfRNA and cfDNA in the cell-free DNA sample; and epigenetic information pertaining to the cell-free DNA, such as hydroxy methylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcy tosine (5mC) residues, respectively. The invention additionally pertains to a classical sequencing-based method for analyzing a biological sample to determine one or more non-classical sequence features of the sample. Compositions, kits, and related methods are also provided, including an embodiment in which truncated sequencing adapters are used in conjunction with barcoded PCR primers.