Barcode Multiplet Identification via Template Sequences
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Solution Overview
Problem
In nucleic acid processing, the current methods often result in lower quality data when multiple barcode sequences are partitioned together, making it difficult to accurately identify which barcodes represent which cell, as the data no longer accurately reflects the nucleic acids present in a particular cell.
Innovation Solution
The method involves using two sets of nucleic acid barcode molecules with different sequences to generate barcoded nucleic acid molecules, which are then sequenced and analyzed to identify the correct partition, allowing for accurate association of barcodes with their respective cells by employing template barcode sequences that interact with other barcode molecules to generate molecules containing both the template and other barcode sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If multiple barcode sequences are partitioned together to increase throughput, then processing efficiency is improved, but data quality deteriorates due to inability to accurately identify which barcodes represent which cell
Solution Approach 1:
The patent segments the barcode identification process by introducing a template barcode sequence that is distinct from cell-derived barcode sequences. This segmentation allows the system to separate and independently analyze template barcodes (which serve as markers for partition identity) from actual cell barcodes, enabling accurate cell identification even when multiple different barcodes are present in the same partition.
Solution Approach 2:
The template barcode sequence acts as an intermediary element that mediates between the partitioning process and the identification process. By incorporating a known template sequence into the barcode molecule, the system creates a reference marker that facilitates the distinction between multiple barcodes in a partition, allowing the system to determine which barcodes originated from the same cell versus those that are merely co-partitioned.
2Speed
If multiple barcode sequences are co-partitioned to increase throughput, then processing speed is improved, but barcode identification accuracy deteriorates
Solution Approach 1:
The patent applies preliminary action by pre-incorporating a known template barcode sequence into the barcode molecule during the partitioning process. This pre-marking with a identifiable template sequence occurs before the actual cell processing and sequencing, enabling later computational distinction between template-derived sequences and cell-derived sequences without requiring additional experimental steps.
Solution Approach 2:
The system employs feedback through computational analysis of sequencing data. By comparing observed barcode sequences against the known template barcode sequence, the system can identify which sequences are template-derived and which are cell-derived. This feedback mechanism allows accurate cell barcode identification even in partitions containing multiple different barcodes, maintaining high identification accuracy while enabling increased throughput.
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 enables accurate identification of nucleic acid origins by generating sequence data that distinguishes between different barcode sequences, resolving the ambiguity of multiple barcodes associated with a single cell and improving data quality.
Implementation Method 1
a first nucleic acid barcode molecule from the first set of barcode molecules comprises a first barcode sequence and a second nucleic acid barcode molecule from the second set of nucleic acid barcode molecules comprises a second barcode sequence
Data Source
AI summary
Methods and systems for processing nucleic acids and identifying the presence of a barcode and barcode bead multiplet event are disclosed. The methods and systems generally may comprise the presence of a support comprising template barcode molecules which may be used to interact with other barcode molecule to generate molecules that comprise multiple barcode sequences. The methods and systems can be applied to a variety of biological samples and can analyze different nucleic acids, proteins, or other macromolecules of the biological samples.