Paired End Sequencing Bead Partitioning for Information Loss
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Solution Overview
Problem
Current methods for paired end sequencing are inefficient and inaccurate, as they often rely on sequencing independent templates randomly, which limits the amount of information obtained from a single template.
Innovation Solution
A method involving the use of two sets of beads, each with a primer complementary to an adaptor on a strand of a biological sample, where the beads are partitioned and subjected to conditions for amplifying the strands, resulting in overlapping copies that enhance sequencing efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If paired end sequencing is performed on two independent templates in a random fashion, then the sequencing process is simpler to implement, but the amount of information obtained is significantly reduced
Solution Approach 1:
The patent merges the sequencing of two strands from a single template by coupling them to the same bead pair, allowing simultaneous amplification and sequencing in the same partition. This combining approach ensures both reads originate from the same template, maximizing information gain while managing complexity through integrated processing.
Solution Approach 2:
The patent segments the template into two strands, each coupled to a different bead (first bead and second bead), which are then partitioned together. This segmentation allows independent amplification of each strand while maintaining their association through the bead pair, enabling parallel processing without losing template context.
2Measurement precision
If two sets of beads with different primers are used for paired end sequencing, then sequencing accuracy and information quality improve, but the complexity of bead preparation and partitioning increases
Solution Approach 1:
The patent uses adaptors as intermediaries that couple the template strands to the beads. Each adaptor contains a primer binding site that specific primers on the beads can anneal to. This intermediary mechanism enables precise primer-template matching and high sequencing accuracy while simplifying the overall process by decoupling the bead design from direct template interaction.
Solution Approach 2:
The patent applies local quality by using different primers on different beads that are specifically complementary to different adaptor regions. This localized specificity ensures each bead targets its intended strand with high precision, improving measurement accuracy while the modular adaptor design manages the complexity of having multiple primer types.
3Productivity
If strands are amplified to generate overlapping copies, then sequencing efficiency and information quality increase, but the amplification conditions and process control become more complex
Solution Approach 1:
The patent performs preliminary action by designing the amplification process to generate overlapping copies of the template strands. The amplification conditions are pre-optimized to ensure that both strands are amplified with sufficient overlap, which facilitates subsequent sequencing and assembly. This preliminary structuring of the amplified products improves sequencing efficiency by ensuring adequate coverage and alignment regions.
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 significantly increases the efficiency and accuracy of paired end sequencing by generating more informative sequence reads from a single template, thereby improving the quality of information obtained from nucleic acid sequencing.
Implementation Method 1
a first bead of the first set of beads comprises a first primer having sequence complementarity with a first adaptor coupled to a first strand of the biological sample
Implementation Method 2
subjecting the partition to conditions sufficient to amplify the first strand and the second strand to generate one or more copies of the first strand coupled to the first bead and one or more copies of the second strand coupled to the second bead
Data Source
AI summary
Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.