Multi-Species DNA Methylation Array for Cross-Species CpG Detection
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Solution Overview
Problem
Current DNA methylation-based arrays are limited to a single species and require costly, time-consuming, and computationally intensive methods for analyzing methylation patterns in non-human technologies have not addressed the need for analyzing methylation patterns in non-human species, and lack of multi-species compatibility in detecting methylation patterns in non-human species, restricting their use to specific species and requiring multiple arrays for different species, which is inefficient and costly.
Innovation Solution
A multi-species chip that includes probes that are complementary to a chip that are specific for CpG sites from multiple species, allowing simultaneous analysis of CpG sites from different animal species, including mammals, birds, and aquatic animals, on a single array, providing faster and cost-effective data generation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional sequencing methods (WGBS or RRBS) are used to analyze methylation patterns in non-human species, then comprehensive methylation data can be obtained, but the process becomes costly, time-consuming, and computationally intensive
Solution Approach 1:
The patent creates a simplified copy of the methylation analysis process using array-based hybridization instead of full sequencing. The array chip contains probes that hybridize to methylated DNA regions, providing a faster and less expensive alternative to WGBS or RRBS while maintaining sufficient measurement precision for detecting methylation patterns in non-human species
Solution Approach 2:
The patent extracts only the most relevant methylation information by designing arrays that target specific CpG sites and methylated regions rather than analyzing the entire genome. This extraction approach retains the essential methylation data needed for species identification and environmental analysis while dramatically reducing computational and temporal requirements
2Measurement precision
If single-species arrays are used for methylation analysis, then species-specific accuracy is maintained, but multiple arrays are required for different species, increasing cost and complexity
Solution Approach 1:
The patent designs a universal multi-species array chip that can detect methylation patterns across multiple animal species simultaneously. The array includes probes for various species (mammals, birds, fish, invertebrates) that hybridize to their respective methylated DNA regions, allowing one array to serve multiple functions for different species analysis
Solution Approach 2:
The patent merges multiple single-species arrays into a single multi-species array by combining probes from different species on one chip. This consolidation maintains species-specific detection accuracy while reducing the total number of arrays needed from multiple separate chips to one integrated array, thereby lowering cost and complexity
3Adaptability or versatility
If conserved CpG sites are used for multi-species arrays, then cross-species compatibility is achieved, but the number of detectable sites is limited to only conserved regions
Solution Approach 1:
The patent applies local quality by designing probes that target specific methylated regions and CpG sites unique to each species rather than relying solely on universally conserved sites. This allows the array to detect species-specific methylation patterns while maintaining cross-species compatibility, thereby increasing the total number of detectable sites across all represented species
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 multi-species chip enables accurate and efficient detection of methylation patterns across multiple species, reducing costs and time by 10x compared to traditional sequencing, while maintaining data quality and computational efficiency.
Implementation Method 1
probes complementary to nucleic acids of CpG sites distinct to more than one animal species
Data Source
AI summary
A DNA methylation-based array includes at least: a first plurality of distinct locations, each location having at least one probe molecule comprising a nucleic acid sequence complementary to a CpG site from a first plurality of CpG sites of a first animal species; and a second plurality of distinct locations, each location having at least one probe molecule comprising a nucleic acid sequence complementary to a CpG site from a second plurality of CpG sites of a second animal species, wherein the first and second animal species are each independently selected from the group consisting of virus, mammals, birds and aquatic animals, and wherein the first plurality of CpG sites comprises at least 1000 CpG sites of the first animal species; and the second plurality of CpG sites comprises at least 1000 CpG sites of the second animal species.