Chimerism Measurement Using Informative Copy Number Variations
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Solution Overview
Problem
Current methods for measuring chimerism in biological samples after hematopoietic stem-cell transplantation (HSCT) are inaccurate and inefficient, particularly in cases where donor and recipient share genetic determinants, and have limitations such as requiring gender mismatch or low sensitivity for early relapse detection.
Innovation Solution
Assessing informative copy number variation (CNV) polymorphisms in genomic DNA to accurately measure chimerism by isolating and quantifying DNA from genetically distinct cell populations using techniques like droplet digital PCR and NanoString technology.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If STR loci analysis by PCR amplification is used to monitor chimerism, then chimerism can be detected, but multiple STR loci must be analyzed to identify differentiating loci especially when donor and recipient are related
Solution Approach 1:
The invention extracts and utilizes copy number variation (CNV) polymorphisms as specific genetic markers to differentiate donor and recipient cells. By focusing on CNV regions rather than analyzing multiple STR loci, the method simplifies the analysis while maintaining high precision in chimerism detection, especially for related donors and recipients who share many genetic determinants.
2Measurement precision
If FISH with X- and Y-specific chromosome probes is used for chimerism monitoring, then cytological distinction of donor and recipient cells is achieved, but it requires gender mismatch between donor and recipient
Solution Approach 1:
The CNV-based method provides a universal approach for chimerism monitoring that works regardless of donor-recipient gender matching. By using autosomal CNV polymorphisms rather than sex chromosome-specific probes, the method can be applied to all transplant scenarios including matched and mismatched pairs, making it universally applicable.
3Measurement precision
If FISH is used for chimerism monitoring, then donor and recipient cells can be distinguished, but the sensitivity is only about >1% which is inadequate for early relapse detection
Solution Approach 1:
The invention changes the detection parameter from visual cytological assessment by FISH to quantitative molecular analysis by PCR. This parameter change enables detection of much lower levels of donor or recipient cells, achieving sensitivity sufficient for early relapse detection while maintaining cell distinction capability.
4Measurement precision
If TaqMan real-time PCR of SNP or indel markers is used for chimerism monitoring, then chimerism can be measured, but each marker has relatively low discrimination power requiring evaluation of large numbers of loci
Solution Approach 1:
The invention focuses on specific local regions of the genome where copy number variations occur. By targeting CNV polymorphisms which represent localized structural variations rather than relying on multiple distributed SNP or indel markers, the method achieves high discrimination power with fewer loci to be evaluated.
Data Source
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AI summary
The present disclosure relates to methods of measuring chimerism in a biological sample using informative copy number variations (CNV).