Nucleic Acid Sequencing With 3D Spatial Barcode Context
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Solution Overview
Problem
Existing polynucleotide sequencing methods fail to retain structural and molecular context of nucleic acid sequences, losing important spatial and contextual information during sample processing.
Innovation Solution
Methods involving nucleic acid extraction, partitioning, barcoding, and sequencing that maintain spatial and molecular context by attributing sequence reads to their original three-dimensional location within the sample, using barcode sequences and optically identifiable tags.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If sequence information is extracted from native genomic DNA, then structural and molecular context is lost, but sequencing can be performed on standard platforms
Solution Approach 1:
The patent creates a copy of the genomic DNA that preserves the structural and molecular context (such as chromatin conformation, protein-DNA interactions, and epigenetic marks) while being suitable for sequencing. This is achieved through methods like chromatin immunoprecipitation (ChIP) followed by library preparation that maintains spatial information, allowing standard sequencing platforms to read the copied information without direct sequencing of native DNA.
Solution Approach 2:
The patent uses an intermediary approach where native genomic DNA is not directly sequenced but rather its information is transferred to a suitable format through intermediate steps. For example, DNA is crosslinked with proteins, fragmented, and then processed through library preparation that preserves interaction information, serving as an intermediary between the native structure and the sequencing platform requirements.
2Measurement precision
If genomic DNA is extracted and processed through multiple steps, then sequence information can be obtained, but time and sample material are lost
Solution Approach 1:
The patent performs preliminary actions by pre-processing the genomic DNA in ways that preserve structural information while preparing it for sequencing. For example, crosslinking proteins to DNA before fragmentation, or performing in situ library preparation that maintains spatial context, so that subsequent sequencing steps can be performed more efficiently without requiring extensive additional processing time.
Solution Approach 2:
The patent merges multiple processing steps into integrated workflows. For example, combining chromatin fragmentation, library preparation, and crosslinking reversal into a streamlined protocol that reduces the number of separate operations, thereby decreasing total processing time while maintaining sequence information accuracy.
3Ease of manufacture
If genomic DNA is sheared into fragments, then library preparation can be performed, but structural context is degraded
Solution Approach 1:
The patent addresses the loss of structural context during fragmentation by preserving information in another dimension. For example, using crosslinked protein-DNA complexes to maintain spatial relationships even after DNA fragmentation, or using proximity ligation methods that restore spatial context in the sequencing library by joining fragments based on their original proximity in the genome.
Data Source
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AI summary
The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.