Unified Omics Profiling via Barcoded Antibody Tagmentation
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Solution Overview
Problem
Current methods for analyzing the epigenome, transcriptome, and proteome of a sample often destroy the sample, making simultaneous, quantitative, and reproducible analysis challenging due to the need for replicate aliquots and limiting inter-assay comparisons.
Innovation Solution
A method involving contacting a cell-containing sample with antigen-binding molecules conjugated to oligonucleotides, tagmenting genomic DNA, isolating mRNA transcripts, generating a cDNA library, and amplifying unique molecular identifier sequences to identify expression, epigenetic, and transcriptional profiles, allowing for simultaneous analysis of these profiles without sample destruction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If next generation sequencing assays are performed on the epigenome, transcriptome, and proteome separately, then each profile can be analyzed in detail, but the sample is destroyed in the process, precluding inter-assay compatibility and requiring replicate aliquots that double or triple sample preparation time
Solution Approach 1:
The patent combines epigenetic, transcriptomic, and proteomic analysis into a single integrated assay using a unified library preparation workflow. By using a single set of barcoded antibodies and a unified sequencing library, all three profiles are obtained from one sample without requiring separate replicate preparations, thereby eliminating the time loss associated with multiple sample preparations while maintaining detailed profiling precision for each omic layer.
Solution Approach 2:
The patent creates a universal assay platform that simultaneously performs epigenetic, transcriptomic, and proteomic profiling through a single library preparation protocol. The universal barcoded antibody system and unified sequencing approach enable one sample to serve multiple analytical purposes, making the assay multi-functional and eliminating the need for separate specialized assays for each omic layer.
2Adaptability or versatility
If replicate aliquots are prepared for multiplexed analysis, then simultaneous analysis of multiple profiles is enabled, but sample availability is constrained and inter-assay comparisons become difficult
Solution Approach 1:
The patent merges epigenetic, transcriptomic, and proteomic analysis into a single integrated assay using a unified library preparation workflow. By using a single set of barcoded antibodies and a unified sequencing library, all three profiles are obtained from one sample without requiring separate replicate preparations, thereby eliminating the time loss associated with multiple sample preparations while maintaining detailed profiling precision for each omic layer.
Solution Approach 2:
The patent changes the fundamental parameter of sample usage from consuming separate replicate aliquots for each assay to using a single sample for all assays. This parameter change is achieved through the unified barcoded antibody approach and integrated library preparation, allowing one sample to provide all three omic profiles simultaneously, thus preserving sample availability while enabling multiplexed analysis.
3Ease of manufacture
If separate assays are performed for epigenome, transcriptome, and proteome analysis, then each profile can be optimized independently, but inter-assay comparisons from the same sample become difficult or impossible
Solution Approach 1:
The patent merges epigenetic, transcriptomic, and proteomic analysis into a single integrated assay using a unified library preparation workflow. By using a single set of barcoded antibodies and a unified sequencing library, all three profiles are obtained from one sample without requiring separate replicate preparations, thereby eliminating the time loss associated with multiple sample preparations while maintaining detailed profiling precision for each omic layer.
Solution Approach 2:
The patent changes the fundamental parameter of sample usage from consuming separate replicate aliquots for each assay to using a single sample for all assays. This parameter change is achieved through the unified barcoded antibody approach and integrated library preparation, allowing one sample to provide all three omic profiles simultaneously, thus preserving sample availability while enabling multiplexed analysis.
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, quantitative, and reproducible analysis of expression, epigenetic, and transcriptional profiles from a single cell or population of cells, improving sample utilization and inter-assay compatibility.
Implementation Method 1
contacting a cell-containing sample with a plurality of antigen-binding molecules under conditions that promote specific binding of the antigen-binding molecules to target antigens of the cells in the sample
Implementation Method 2
The method also may include analyzing the amplified unique molecular identifier sequences and antigen-binding molecule identifier sequences to identify at least one target antigen in the second fraction
Implementation Method 3
generating a cDNA library by reverse transcribing the mRNA transcripts in the first fraction
Implementation Method 4
tagmenting genomic DNA in the cells to produce a plurality of tagmented double-stranded genomic DNA fragments comprising an oligonucleotide adaptor sequence at the 5′ end of each genomic DNA fragment
Implementation Method 5
amplifying (i) the unique molecular identifier sequences; (ii) the antigen-binding molecule identifier sequences; (iii) the assay molecule identifier sequences, and the (iv) tagmented genomic DNA fragments in the second fraction
Data Source
AI summary
Provided herein are methods for identification of an expression profile, a transcriptional profile, and/or an epigenetic profile from a cell-containing sample. Also provided are compositions for use in the disclosed methods.