Nucleic Acid Sequencing With Partitioned Barcoding for Cell Attribution
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Solution Overview
Problem
Existing nucleic acid sequencing technologies struggle to identify and characterize sub-populations of cells in biological samples, particularly those representing a minority of the overall sample, due to ensemble processing methods that bias towards majority constituents and fail to preserve the starting ratios of minority components, leading to inaccurate data and the inability to attribute genetic material to specific cells.
Innovation Solution
The method involves compartmentalizing nucleic acids from individual cells or small populations into discrete partitions, attaching unique barcodes to these nucleic acids, and characterizing them to attribute the sequences back to their originating cells, using microfluidic systems and bead-based barcoding to ensure accurate sequencing and analysis of minority cell types.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If ensemble processing methods are used for nucleic acid sequencing, then high-throughput sequencing is achieved, but the ability to identify and characterize sub-populations of cells is lost
Solution Approach 1:
The patent segments the sequencing process by partitioning individual cells or small populations into discrete partitions, each with its own barcode. This allows high-throughput sequencing to be maintained while enabling precise identification of sub-populations through barcode-based tracking of individual cell lineages.
Solution Approach 2:
The patent introduces barcode oligonucleotides as intermediaries that are attached to nucleic acids from individual cells. These barcodes serve as mediators between the individual cell level and the sequencing analysis level, enabling attribution of sequencing data to specific cells while maintaining high-throughput processing.
2Productivity
If ensemble processing methods are used, then sequencing efficiency is improved, but the starting ratios of minority components are not preserved
Solution Approach 1:
By segmenting the sample into discrete partitions containing individual cells or small populations, the method preserves the starting ratios of minority components. Each partition maintains the original cellular composition, allowing accurate representation of minority cell types throughout the sequencing process.
Solution Approach 2:
The patent creates molecular copies of nucleic acids from individual cells while attaching barcodes. These barcode-linked copies preserve the original cellular ratios and can be amplified and sequenced without losing the starting composition information of minority components.
3Quantity of substance
If conventional sequencing methods are used, then cost is reduced, but the ability to attribute genetic material to specific cells is lost
Solution Approach 1:
The patent uses barcode oligonucleotides as intermediaries that carry cell attribution information. These barcodes are attached to nucleic acids from individual cells and remain attached through amplification and sequencing, enabling cost-effective analysis of low amounts of nucleic acids while preserving cell attribution information.
Solution Approach 2:
The barcode oligonucleotides serve multiple functions: they act as primers for amplification, carry cell identification information, and enable sequencing. This multi-functionality allows cost-effective analysis of low input amounts while maintaining attribution capability.
Data Source
AI summary
The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.