RNA Expression Mapping Across Sequencing Protocols
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Solution Overview
Problem
Current techniques fail to effectively address batch effects in gene expression levels when comparing samples processed using different protocols, limiting the compatibility and comparability of nucleic acid sequencing data, particularly in precision medicine applications where biomarkers depend on gene expression levels obtained using different methodologies.
Innovation Solution
A method using computer hardware processors to map RNA expression levels from one protocol to those that would have been determined using another protocol, employing transformations such as linear or non-linear regression to adjust data, allowing for compatibility and comparison of sequencing data from different sample preparation and sequencing techniques.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If different sequencing protocols are used to process biological samples, then diverse sample preparation and sequencing techniques can be utilized, but batch effects arise that prevent direct comparison of gene expression levels
Solution Approach 1:
The patent introduces reference genes as intermediary elements that are present across all protocols. These reference genes serve as a common baseline to mediate between different sequencing protocols, enabling the transformation of expression levels from one protocol to another through ratio calculations that eliminate protocol-specific biases
Solution Approach 2:
The patent transforms expression level measurements by changing the reference parameter from protocol-specific housekeeping genes to universal reference genes. This parameter change allows expression levels to be normalized across different protocols, making them comparable despite differences in sample preparation and sequencing methodologies
2Measurement precision
If reference cohorts are established using a specific sequencing protocol, then accurate baseline comparisons can be made, but samples processed with different protocols cannot be directly compared to the cohort
Solution Approach 1:
Reference genes act as intermediaries that bridge the gap between single samples processed with one protocol and reference cohorts processed with another protocol. By using these common reference points, the patent enables accurate comparison across protocol boundaries while maintaining the integrity of the reference cohort
Solution Approach 2:
The patent creates a universal comparison framework where reference genes serve multiple functions: they are used both in single-sample analysis and in reference cohort establishment. This universality allows any sample from any protocol to be compared against the reference cohort through a common normalization pathway
3Reliability
If traditional batch correction methods are applied to multiple samples, then batch effects between large cohorts can be reduced, but single samples cannot be effectively corrected
Solution Approach 1:
The patent segments the batch correction approach into gene-specific transformations based on reference gene ratios. Instead of applying a single correction factor to all genes in a batch, the method calculates individual transformation factors for each gene using reference gene comparisons, enabling effective correction even for single samples
Solution Approach 2:
The patent creates a virtual copy of the reference cohort's expression profile for the single sample being analyzed. By transforming the single sample's expression levels to match the protocol used in the reference cohort, the method effectively copies the normalization approach from multi-sample batch correction to single-sample correction
Data Source
AI summary
Aspects of the disclosure relate to methods for improving compatibility of nucleic acid sequencing data obtained using different techniques. The disclosure is based, in part, on methods for mapping expression levels for genes expressed in a biological sample and obtained from a subject using a first protocol to expression levels as would have been determined through a second protocol if the second protocol were used to process the biological sample instead of the first protocol.