Maternal Plasma Transcriptome Analysis via Massively Parallel RNA Sequencing
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Solution Overview
Problem
Current methods for directly profiling extracellular RNA in maternal plasma are limited due to low concentrations and degradation, making it difficult to identify RNA markers for fetal disorders and pregnancy-related pathologies, and are not effective in distinguishing between RNA molecules from two individuals, such as in organ transplantation scenarios.
Innovation Solution
The use of massively parallel sequencing (MPS) for RNA analysis, specifically RNA-seq, allows for the direct profiling of maternal plasma transcriptome by identifying and analyzing allele-specific expression patterns, enabling the differentiation between fetal and maternal RNA contributions and diagnosing pregnancy-associated disorders.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional high-throughput screening technologies (microarray analysis and SAGE) are used to directly profile extracellular RNA in maternal plasma, then the screening capacity is provided, but the detection ability is insufficient due to low concentrations and degradation of RNA molecules
Solution Approach 1:
The patent changes the detection parameter from conventional microarray/SAGE methods to massively parallel sequencing (RNA-seq), which provides both high throughput screening capacity and enhanced sensitivity for detecting low-concentration degraded RNA molecules in maternal plasma
Solution Approach 2:
The patent replaces the mechanical hybridization-based detection system (microarray) with a sequencing-based detection system (RNA-seq), which uses biochemical enzymatic reactions and next-generation sequencing technology to achieve superior detection sensitivity while maintaining high throughput
2Measurement precision
If indirect method comparing placenta and maternal blood cell expression profiles is used, then some RNA markers are identified, but the methodology cannot fully account for all biological factors and misses non-placental tissue transcripts
Solution Approach 1:
Instead of indirectly inferring plasma RNA markers by comparing tissue expression profiles, the patent inverts the approach by directly sequencing and profiling the actual extracellular RNA molecules present in maternal plasma, thereby capturing all biological factors including non-placental tissue contributions
Solution Approach 2:
The patent extracts and directly analyzes the extracellular RNA molecules from maternal plasma itself, rather than relying on inference from tissue samples, thereby obtaining authentic representation of all RNA sources including placenta, maternal tissues, and fetal contributions
3Measurement precision
If tissue-based mining strategy is used to identify plasma RNA markers, then placental transcripts are identified, but the strategy fails to identify transcripts from non-placental tissues released in response to pregnancy
Solution Approach 1:
The patent applies a universal direct sequencing approach that can detect RNA molecules from any tissue source (placenta, maternal tissues, fetal tissues) simultaneously, rather than being limited to placental-specific markers identified through tissue-based mining strategies
4Measurement precision
If real-time RT-PCR is used for high sensitivity detection, then individual transcripts can be analyzed, but the throughput is limited and cannot profile the entire transcriptome
Solution Approach 1:
The patent merges the high sensitivity detection capability of PCR-based methods with the high throughput of sequencing technology by using RNA-seq, which simultaneously achieves both sensitive detection of individual transcripts and comprehensive profiling of the entire transcriptome through massively parallel sequencing
Data Source
AI summary
Methods are provided for diagnosing pregnancy-associated disorders, determining allelic ratios, determining maternal or fetal contributions to circulating transcripts, and/or identifying maternal or fetal markers using a sample from a pregnant female subject. Also provided is use of a gene for diagnosing a pregnancy-associated disorder in a pregnant female subject.