Genomic Profiling via Flow Sorting of FFPE Nuclei
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Solution Overview
Problem
Current methods for genomic profiling of heterogeneous and polyclonal neoplastic cell populations from formalin-fixed paraffin-embedded (FFPE) samples face challenges due to poor DNA quality and tissue heterogeneity, limiting the effective use of FFPE samples in next-generation sequencing and high-resolution genetic profiling.
Innovation Solution
A system and method involving flow sorting of de-agglomerated nuclei based on genetic material quantification, followed by differential labeling, comparative genomic hybridization, and aberration detection algorithms to identify unique aberrations in cancer cell genomes, which includes DNA extraction, amplification, and sequencing of FFPE samples to infer tumor evolution and select therapeutic agents.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If high number reads (>100×) are used in next-generation sequencing to overcome tissue heterogeneity, then the ability to detect genomic aberrations improves, but errors associated with poor quality samples are exacerbated
Solution Approach 1:
The patent extracts and isolates individual neoplastic cells from heterogeneous tissue samples using microdissection and flow cytometry techniques. By separating target cells from the mixed population before sequencing, the method eliminates the need for high read numbers to overcome heterogeneity, thereby reducing error rates while maintaining detection accuracy.
Solution Approach 2:
The patent segments the tissue sample into individual cells or nuclei, then further segments them into pure neoplastic cell populations through sorting techniques. This segmentation approach transforms the analysis from bulk tissue to purified cell populations, enabling accurate genomic profiling without requiring excessive sequencing depth to filter out normal cell signals.
2Adaptability or versatility
If FFPE samples are used for genomic analysis, then the availability of archived clinical samples with patient follow-up data improves, but the quality of DNA extracted from these samples deteriorates
Solution Approach 1:
The patent applies preliminary enrichment actions by isolating and purifying neoplastic cells from FFPE samples before DNA extraction and sequencing. By performing cell sorting and microdissection upfront, the method compensates for DNA degradation in FFPE samples, ensuring sufficient quality for genomic analysis while maintaining the advantage of using archived clinical specimens.
3Ease of manufacture
If bulk extraction methods are used for FFPE samples, then the simplicity of the extraction process improves, but the signal to noise level deteriorates due to heavy admixtures of normal and tumor cells
Solution Approach 1:
The patent extracts and separates neoplastic cells from the bulk tissue sample using microdissection and flow cytometry before performing DNA extraction. This preliminary extraction of target cells from the admixed population dramatically improves the signal-to-noise ratio in subsequent genomic analyses, allowing for precise detection of tumor-specific aberrations while maintaining a streamlined overall workflow.
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
This approach enables high-resolution genomic analysis and improved identification of aberrations in FFPE samples, enhancing the ability to differentiate between clonal populations and infer tumor evolution, thereby facilitating personalized therapeutic strategies.
Implementation Method 1
sorting the nuclei into a plurality of fractions based at least on a quantification of genetic material in the nuclei
Implementation Method 2
flow sorting of de-agglomerated nuclei based on genetic material quantification
Implementation Method 3
hybridizing the labeled extracted genetic material and reference sample on a feature comparative genomic hybridization array
Data Source
AI summary
The present invention relates to a system and method of genomic profiling and is particularly useful in genomic differentiation of heterogeneous and polyclonal neoplastic cell populations, preferably of flow sorted formalin fixed paraffin embedded samples. The present invention includes methods of improving resolution for identifying aberration in variable carcinoma genomes and/or heterogeneous cell populations. The present invention also includes kits configured to improve genomic resolution and the ability to identify genomic aberration in variable and/or heterogeneous cell populations.