Cell-free DNA Methylation Detection via Fragmentation Patterns
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Solution Overview
Problem
Current methods for identifying the tissue of origin for circulating tumor DNA (ctDNA) face challenges such as the need for deep coverage bisulfite sequencing, limited reference nucleosome maps, and DNA degradation during library preparation, which hinder their clinical application.
Innovation Solution
A method involving whole-genome sequencing of cell-free DNA (cfDNA) and genomic DNA (gDNA), where alterations in fragmentation patterns are detected to identify DNA methylation patterns with single base pair resolution, allowing for the determination of the tissue of origin using a Bayesian non-homogeneous Hidden Markov Model.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If deep coverage bisulfite sequencing is used to identify DNA methylation patterns, then measurement precision is improved, but device complexity and cost increase
Solution Approach 1:
The patent extracts and analyzes only the fragmentation pattern information from whole genome sequencing data, rather than performing deep coverage bisulfite sequencing. By focusing on fragment length, coverage, and distance to fragment end, the method obtains DNA methylation patterns without requiring deep sequencing coverage or bisulfite conversion procedures.
Solution Approach 2:
The patent makes whole genome sequencing data serve multiple functions: it simultaneously provides genomic information and DNA methylation pattern information through fragmentation pattern analysis. This eliminates the need for separate bisulfite sequencing experiments, reducing both complexity and cost while maintaining measurement precision.
2Measurement precision
If whole genome bisulfite sequencing is performed on low-input DNA samples, then measurement precision is improved, but DNA degradation increases
Solution Approach 1:
The patent converts the naturally occurring fragmentation of cfDNA, which is typically seen as a limitation, into a useful signal for detecting DNA methylation patterns. By analyzing fragment length, coverage, and distance to fragment end, the method transforms DNA degradation into a source of information about methylation status without requiring additional DNA damage.
3Adaptability or versatility
If reference nucleosome maps are expanded to cover more tissue types, then adaptability is improved, but device complexity and data processing requirements increase
Solution Approach 1:
The patent enables the system to generate its own reference fragmentation patterns directly from whole genome sequencing data without requiring external nucleosome maps. The method uses the sequencing data itself to establish baseline fragmentation characteristics, making the analysis self-sufficient and adaptable to any tissue type without expanding reference databases.
Data Source
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Figure 1B-2
AI summary
As described below, disclosed herein are methods of analyzing DNA methylation in cell-free DNA (cfDNA) and genomic DNA (gDNA) from sequencing data.