Multiplex DNA Detection for CHIP Risk via Hybridization Capture
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for detecting Clonal Hematopoiesis of Indeterminate Potential (CHIP) are costly and inefficient, requiring whole genome or exome sequencing, which is not scalable for widespread application.
Innovation Solution
A scalable multiplex method for amplifying and sequencing target DNA regions, including genes associated with CHIP, using DNA library preparation techniques such as mechanical or enzymatic fragmentation, end repair, dA-tailing, ligation of universal adapters, normalization, and hybridization capture, followed by PCR amplification and sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If whole genome or exome sequencing is used to detect CHIP mutations, then measurement precision is improved, but device complexity and cost increase significantly
Solution Approach 1:
The patent segments the genome into specific target regions containing CHIP-associated genes (DNMT3A, TET2, ASXL1, JAK2, GNAS, GNB, CBL, TP53, PPM1D, SF3B1, SRSF2, PIGA, BCOR, BCORL1) and uses hybridization capture to selectively enrich these regions. This segmentation approach maintains detection precision for relevant mutations while reducing the complexity and cost associated with whole genome or exome sequencing by focusing only on clinically significant regions.
2Measurement precision
If whole genome or exome sequencing is used to detect CHIP mutations, then measurement precision is improved, but productivity decreases due to cost and scalability limitations
Solution Approach 1:
By segmenting the genome into specific target regions and using hybridization capture with biotinylated RNA or DNA probes, the method enables scalable multiplex detection. The captured regions can be amplified and sequenced efficiently, allowing high-throughput processing of multiple samples simultaneously while maintaining precision for CHIP mutation detection.
Solution Approach 2:
The patent uses PCR amplification to generate multiple copies of the captured target DNA regions before sequencing. This copying step increases the amount of template available for sequencing, improving productivity and enabling scalable processing of many samples without requiring whole genome sequencing of each individual sample.
3Manufacturing precision
If hybridization capture with biotinylated probes is used, then manufacturing precision is improved for target enrichment, but device complexity increases
Solution Approach 1:
The patent uses biotinylated RNA or DNA probes as intermediaries to mediate the capture of target DNA regions. These probes hybridize specifically to complementary sequences in the fragmented and adapter-ligated DNA library, enabling precise enrichment of target regions. The biotin tag on the probes allows for easy capture using streptavidin-coated magnetic beads, simplifying the separation process despite the added step.
Solution Approach 2:
The patent replaces traditional mechanical separation methods with magnetic bead-based capture. Streptavidin-coated magnetic beads bind to the biotinylated probes, allowing target enrichment to be performed using magnetic field manipulation rather than mechanical centrifugation or filtration. This substitution improves precision while managing complexity through standardized magnetic separation protocols.
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 method allows for efficient detection of mutations indicative of CHIP, enabling identification of subjects at increased risk for cardiometabolic diseases and hematological cancers, thereby facilitating targeted therapeutic approaches.
Implementation Method 1
hybridization capturing dA-tailed DNA fragments in the DNA target regions from the normalized barcoded-DNA library
Data Source
AI summary
Disclosed herein is a scalable multiplex method for amplifying a plurality of target DNA regions collectively 1 kb to 100 kb in size in a plurality of samples. Also disclosed herein is a scalable multiplex method for identifying a subject with increased risk of developing a cardiometabolic disease or a hematological cancer that involves amplifying and sequencing target DNA regions corresponding to the genes DNMT3A, TET2, ASXL1, JAK2, GNAS, GNB, CBL, TP53, PPM1D, SF3B1, SRSF2, PIGA, BCOR, BCORL1, DNMT3A, and ASXL1 from a plurality of DNA samples according to the method disclosed herein, and identifying from said sequencing one or more mutations in one or more of the genes, wherein presence of said mutation(s) indicates an increased risk of developing a cardiometabolic disease and/or a hematological cancer.