One-Sided DNA Transposition for Haplotype-Preserving Sequencing
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Solution Overview
Problem
Next generation sequencing technologies face challenges in maintaining contiguity, phasing, and haplotype information during genomic DNA fragmentation due to the use of traditional fragmentation methods, leading to loss of information regarding individual nucleic acid molecules.
Innovation Solution
One-sided transposition is performed by nicking only one strand of a double-stranded target DNA, allowing the target DNA to remain intact after transposition, thereby preserving contiguity and haplotype information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional fragmentation methods are used for genomic DNA, then the DNA is broken into smaller fragments suitable for sequencing, but contiguity and haplotype information are lost
Solution Approach 1:
The transposome system segments the genomic DNA into smaller fragments through transposition events, making the DNA suitable for next-generation sequencing while maintaining the ability to track original molecular relationships through adapter sequences
Solution Approach 2:
Adapter sequences serve as intermediaries that are introduced during transposition, allowing the fragmented DNA to retain contiguity information. These adapters act as molecular tags that link fragmented sequences back to their original parental molecule
2Productivity
If traditional fragmentation methods are used for genomic DNA, then the DNA is broken into smaller fragments suitable for sequencing, but phasing and haplotype information are lost
Solution Approach 1:
Unique molecular identifiers (UMIs) and adapter sequences act as intermediaries that tag individual DNA molecules during transposition. These tags preserve haplotype information by allowing reconstruction of which variants co-occur on the same original molecular strand
Solution Approach 2:
The transposition process introduces different types of molecular tags at different locations within the fragmented DNA. UMIs are incorporated at specific sites to track individual molecules, while adapters are added at fragment ends for sequencing, creating localized functional differences that preserve global molecular identity
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
The method maintains contiguity and haplotype information by ensuring the target DNA remains intact, enabling accurate sequencing and capturing of phasing and haplotype information.
Implementation Method 1
a transposome comprising a transposase and a transposon nucleic acid wherein the transposome is configured to nick and transfer the transposon to only one strand of the target nucleic acid
Data Source
AI summary
Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.