Nucleic Acid Analysis Using Reflex Process for Long Fragment Linkage
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Solution Overview
Problem
Current DNA sequencing technologies face limitations in analyzing fragments longer than their sequencing capacity and fail to maintain linkage information between sequence changes in different parts of a genomic region due to fragmentation, leading to incomplete analysis and loss of linkage data.
Innovation Solution
The reflex process involves moving a region of interest within a polynucleotide from one position to another, allowing functional elements like primer sites and MID tags to be positioned in proximity, enabling the analysis of long fragments and maintaining linkage information through intramolecular rearrangement.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If DNA fragments are sequenced using current sequencing technologies, then sequencing can be performed, but fragments longer than the sequencing capacity cannot be fully analyzed and linkage information is lost
Solution Approach 1:
The patent applies segmentation by dividing long DNA fragments into smaller sub-fragments that can be sequenced individually, then using reflex sequences to reassemble and link these sub-fragments back to the original long fragment, thereby achieving complete analysis of long fragments while maintaining linkage information
Solution Approach 2:
The patent uses reflex sequences as intermediary elements that are introduced into the DNA fragments. These reflex sequences serve as mediators that enable the connection between sequenced sub-fragments and the original long fragment structure, allowing linkage information to be preserved through the sequencing process
2Productivity
If DNA is fragmented for sequencing, then sequencing can proceed, but linkage information between sequence changes in different parts of the genome is lost
Solution Approach 1:
Reflex sequences serve as intermediary markers that are embedded in the fragmented DNA. These intermediaries carry linkage information through the sequencing process, allowing the reassembly of fragments while maintaining the original genomic context and relationships between different sequence changes
Solution Approach 2:
The patent uses the reflex sequence copying mechanism where the reflex sequence is copied and preserved across multiple fragments during the sequencing process. This copying ensures that linkage information is replicated and maintained, allowing accurate reconstruction of the original genomic relationships
Data Source
AI summary
Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.