Paired Code Tags for De Novo Nucleic Acid Assembly
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current nucleic acid sequencing methods face challenges in assembling contiguous reads, especially through repetitive sequences, requiring larger DNA amounts and a reference genome for verification, and often result in lost order information during DNA fragmentation.
Innovation Solution
The method involves preparing a library of template nucleic acids by inserting unique barcodes into target nucleic acids, fragmenting them, and using paired barcode sequences to assemble sequencing data without a reference genome, preserving order information and enabling de novo assembly of target nucleic acids.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If DNA fragmentation is performed for sequencing, then sequencing throughput is improved, but order information is lost
Solution Approach 1:
The DNA molecule is segmented into multiple fragments through controlled fragmentation, with each fragment receiving a unique molecular identifier (UMI) barcode. This segmentation enables parallel processing of multiple fragments simultaneously, improving sequencing throughput while the barcodes preserve the original positional information for later reassembly.
Solution Approach 2:
Unique molecular identifier (UMI) barcodes serve as intermediary tags that are attached to each DNA fragment during library preparation. These barcodes act as mediators that carry positional information through the fragmentation and sequencing process, enabling reconstruction of the original DNA sequence order after high-throughput sequencing.
2Measurement precision
If traditional assembly methods are used for repetitive sequences, then assembly accuracy is improved, but a reference genome is required
Solution Approach 1:
The method creates multiple copies of the original DNA sequence information through the use of UMI barcodes on different fragments. By sequencing multiple barcoded fragments that originate from the same genomic region, the system can reconstruct repetitive sequences de novo without requiring a reference genome, achieving high assembly accuracy through redundant information copying.
3Reliability
If larger DNA amounts are used for sequencing, then coverage is improved, but sample requirements increase
Solution Approach 1:
The UMI barcode system serves multiple functions simultaneously: it tracks individual DNA molecules through fragmentation, enables high-throughput parallel sequencing, preserves positional information for assembly, and allows for de novo reconstruction without reference genomes. This multi-functionality achieves high coverage reliability without proportionally increasing DNA input requirements.
Data Source
AI summary
Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids.