Processed RNA Sample Preparation with Housekeeping Gene Removal
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Solution Overview
Problem
RNA sequencing data is often dominated by house-keeping genes, making it difficult to detect disease-specific genes and generating redundant data, which increases costs and storage requirements, limiting its applications in diagnostics and treatment tracking.
Innovation Solution
Processing RNA samples from blood without fragmentation to capture full-length sequences, allowing identification of cell/tissue of origin and disease-specific protein isoforms, enabling the development of RNA vaccines and biomarker discovery.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If RNA sequencing is performed on total RNA samples, then comprehensive transcriptome coverage is achieved, but house-keeping genes dominate the sequencing data making it difficult to detect disease-specific genes
Solution Approach 1:
The patent extracts and removes house-keeping genes from the RNA sample before sequencing. This is achieved through specific molecular biology techniques that identify and separate house-keeping gene transcripts from the total RNA population, allowing disease-specific genes to be detected without being overwhelmed by the abundant house-keeping gene sequences.
Solution Approach 2:
The patent applies different processing treatments to different portions of the transcriptome. House-keeping genes are targeted for removal or reduction, while disease-specific genes are preserved and enhanced for detection. This differential processing improves the relative abundance and detectability of low-abundance disease-specific transcripts.
2Measurement precision
If sequencing depth is increased to detect low abundance genes, then detection sensitivity improves, but cost and time requirements increase significantly
Solution Approach 1:
By extracting and removing house-keeping genes from the sample prior to sequencing, the patent enriches the remaining pool for low-abundance disease-specific genes. This enrichment means that standard sequencing depths can detect disease genes that would otherwise require much deeper (more expensive and time-consuming) sequencing.
Solution Approach 2:
The patent performs preliminary enrichment of disease-specific transcripts by removing competing house-keeping genes before the sequencing step. This pre-processing action improves detection sensitivity without requiring increased sequencing depth, thereby maintaining cost and time efficiency.
3Loss of substance
If full-length RNA sequencing is performed without fragmentation, then data redundancy is reduced and storage requirements decrease, but detection of low abundance genes becomes more challenging
Solution Approach 1:
The patent removes house-keeping genes from the RNA sample before performing full-length sequencing. This extraction step reduces the overall redundancy in the data by eliminating the most abundant, non-informative transcripts, allowing full-length sequencing to be performed efficiently while still enabling detection of low-abundance disease-specific genes.
Solution Approach 2:
The patent changes the compositional parameters of the RNA sample by removing house-keeping genes, which alters the relative abundance distribution. This parameter change enables full-length sequencing to achieve both reduced redundancy and improved detection of low-abundance genes, as the sequencing capacity is now distributed among fewer, more informative transcripts.
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
Enables efficient detection of disease-specific RNA sequences and protein isoforms, reducing data redundancy and storage needs, facilitating RNA vaccine development and continuous monitoring.
Implementation Method 1
sequencing the processed RNA or cDNA
Implementation Method 2
detecting RNA from all these sources and at full length the invention enables each RNA to be ascribed to a cell/tissue of origin
Data Source
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AI summary
Methods for determining a set of RNA sequences associated with a disease and producing a database of RNA sequences associated with a disease are provided. Methods for discovering disease biomarkers and diagnosing disease are also provided. The present invention also provides methods for processing RNA and cDNA sequences and uses of these methods. Methods for producing RNA vaccines are also provided.