Bead-Based Clonal Amplification for Cost-Effective Sequencing
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Solution Overview
Problem
Current methods for cataloging human genetic variation and correlating it with disease susceptibility are costly and inefficient, with genome sequencing costing around $50,000 per sequence, necessitating a reduction in costs to achieve $1,000 per sequence, and existing methods for creating targeted DNA libraries are cumbersome and expensive.
Innovation Solution
The development of compositions and methods using clonal objects, such as DNA balls, affinity bound or hybridized to beads through patches on the bead surface, allowing for efficient and cost-effective nucleic acid sequence analysis by enabling highly parallelized library generation and amplification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional single-plex PCR is used for each exon, then sequence analysis can be performed, but the cost becomes prohibitively expensive
Solution Approach 1:
The patent combines multiple PCR reactions for different exons into a single parallel reaction by attaching different primer sets to different beads. This merging of previously separate operations into one simultaneous reaction enables cost-effective sequencing of multiple exons without requiring individual single-plex PCR for each exon, directly resolving the cost prohibitive issue while maintaining sequence analysis precision
2Quantity of substance
If clonal amplification is performed traditionally from plasmids, then DNA can be amplified, but the process is time-consuming and expensive
Solution Approach 1:
The patent uses bead-based clonal amplification where beads serve as templates for generating multiple DNA copies simultaneously. This copying approach replaces the traditional time-consuming process of picking individual bacterial colonies and growing plasmids, enabling rapid amplification of multiple DNA sequences in parallel without requiring extended cultivation time
Solution Approach 2:
The patent performs preliminary attachment of primer sets to beads before the amplification process. This preliminary preparation allows the amplification reaction to proceed directly without requiring prior colony picking or plasmid isolation steps, significantly reducing the time needed for DNA amplification while maintaining adequate DNA quantity
3Adaptability or versatility
If targeted library generation is performed using current methods, then specific DNA regions can be selected, but the process is cumbersome
Solution Approach 1:
The patent segments the targeted DNA selection process into discrete bead-based units, where each bead carries specific primer sets for particular exons. This segmentation allows independent selection and amplification of different DNA regions without requiring complex multi-step protocols, simplifying the overall process while maintaining the ability to target specific genomic regions adaptably
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 sequencing costs by enabling the creation of targeted DNA libraries and clonal amplifications in a highly parallel manner, improving the efficiency and cost-effectiveness of genomics analysis, particularly in resequencing cancer genomes.
Implementation Method 1
the clonal object is affinity bound or hybridized to the bead through a patch on the surface of the bead, such as an affinity binding patch or a hybridization patch
Implementation Method 2
the clonal object is affinity bound or hybridized to the bead through a patch on the surface of the bead
Data Source
AI summary
The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein.