Nucleic Acid Deconvolution via Synthetic Target Sequences
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Solution Overview
Problem
Current methods for identifying individual nucleotide sequences in substance mixtures require complex sample preparation, including isolation and purification, which are time-consuming and costly, especially when no significant enrichment of nucleic acids is present, and often necessitate additional verification steps due to factors like plasmid transformation and sequencing processes.
Innovation Solution
A method involving the generation of synthetically designed target nucleotide sequences (TNS) that are chemically coupled to substances, allowing for simultaneous sequencing of multiple TNS in a mixture, followed by deconvolution using signal intensity analysis to identify specific sequences without the need for amplification or isolation, by scanning sequence positions with increased signal intensity and subtracting overlapping signals.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If complex sample preparation including isolation and purification is performed, then sequencing accuracy is improved, but time consumption and cost increase
Solution Approach 1:
The patent applies preliminary action by designing and synthesizing target nucleotide sequences (TNS) with unique barcodes before the selection experiment. These pre-designed TNS are chemically coupled to substances of interest, creating a library where each substance has a known, unique nucleotide identifier. This preliminary preparation eliminates the need for complex post-selection isolation and purification, as the unique barcodes allow direct deconvolution of sequencing data to identify enriched substances.
2Measurement precision
If complex sample preparation including isolation and purification is performed, then sequencing accuracy is improved, but cost increases
Solution Approach 1:
The patent applies preliminary action by designing and synthesizing target nucleotide sequences (TNS) with unique barcodes before the selection experiment. These pre-designed TNS are chemically coupled to substances of interest, creating a library where each substance has a known, unique nucleotide identifier. This preliminary preparation eliminates the need for complex post-selection isolation and purification, as the unique barcodes allow direct deconvolution of sequencing data to identify enriched substances.
3Reliability
If additional verification steps are performed to check enriched substances, then identification reliability is improved, but time consumption increases
Solution Approach 1:
The patent applies feedback by implementing a deconvolution process that uses the unique barcode sequences from sequencing data to directly identify and verify enriched substances. The system cross-references the sequenced barcode sequences with the original library catalog, providing immediate verification of which substances were enriched during the selection experiment. This feedback mechanism eliminates the need for separate verification steps while maintaining high identification reliability.
4Measurement precision
If normal sequencing methods with low parallelisation capacity are used, then sequencing accuracy is maintained, but device complexity and sample preparation complexity increase
Solution Approach 1:
The patent applies universality by designing a system where a single sequencing run can simultaneously sequence multiple unique barcode sequences from different target nucleotide sequences. The deconvolution methodology processes all barcode sequences in parallel by analyzing the sequencing data as a collective set, allowing the system to identify multiple enriched substances in one experiment. This multi-functional approach eliminates the need for separate preparation and sequencing steps for each substance.
Data Source
AI summary
A method for the deconvolution of nucleic acid-containing substance mixtures using synthetically generated target nucleotide sequences. Starting from a plurality of nucleotides,, a plurality of different target nucleotide sequences (TNS) is generated according to a predetermined algorithm. At least one of the TNS generated is associated with at least one substance or substance combination and chemically coupled thereto. At least one substance mixture to be analysed and having at least two different TNS is provided and is sequenced according to a sequencing method., at the same time all TNS contained in the substance mixture are detected in a common sequence spectrum. To facilitate the deconvolution, the sequence spectra of a substance mixture should be deducted/subtracted from each other prior to and after a selection experiment.