Long-Read Nucleic Acid Libraries With Immobilized Transposome Tagging
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current nucleic acid library preparation methods for next-generation sequencing are inefficient, tedious, and expensive, often requiring multiple steps and expensive instruments, and can result in underrepresentation of certain genomic portions.
Innovation Solution
A method involving immobilized transposomes on a solid support, such as beads, to fragment and tag nucleic acids, followed by amplification and addition of library adapters, with optional mutagenesis and suppression PCR, and enrichment using selection probes to target specific sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If transposomes are immobilized on a solid support for library preparation, then preparation time and cost are reduced, but the representation of certain genomic portions may be underrepresented
Solution Approach 1:
The patent applies local quality by using immobilized transposomes with specific spatial distribution on solid supports to create localized tagmentation zones. This allows different regions of the nucleic acid sample to experience controlled fragmentation patterns, improving both preparation efficiency and genomic representation uniformity by addressing specific local requirements rather than applying uniform treatment throughout
2Measurement precision
If multiple steps and instruments are used for library preparation, then sequencing accuracy is improved, but the process becomes more complex and expensive
Solution Approach 1:
The patent merges multiple library preparation steps into a single integrated process using immobilized transposomes. The transposomes simultaneously perform fragmentation, adapter ligation, and enrichment functions that traditionally required separate instruments and steps. This consolidation maintains sequencing accuracy while dramatically reducing process complexity and cost
3Productivity
If standard transposome density is used, then library preparation is faster, but certain genomic regions become underrepresented
Solution Approach 1:
The patent applies dynamics by making the transposome density adjustable and adaptable during the library preparation process. The immobilized transposomes can be distributed at varying densities across the solid support surface, allowing the system to dynamically optimize tagmentation efficiency for different genomic regions. This dynamic approach maintains high preparation speed while ensuring uniform genomic coverage
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
This approach reduces preparation time and cost, enhances representation of underrepresented genomic regions, and allows for efficient generation of long read nucleic acid libraries from short reads.
Implementation Method 1
nucleic acid fragment libraries may be prepared using a transposome-based method where two transposon end sequences, one linked to a tag sequence, and a transposase form a transposome complex. The transposome complexes are used to fragment and tag target nucleic acids in solution
Implementation Method 2
amplifying the plurality of polynucleotides to obtain amplified polynucleotides
Implementation Method 3
enriching for certain sequences in the long fragments with selection probes directed to an American College of Medical Genetics (ACMG) panel of genes
Data Source
AI summary
Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to an American College of Medical Genetics (ACMG) panel of genes. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.