Carrier Status Determination via Molecular Inversion Probes
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Solution Overview
Problem
Current carrier screening assays, such as MLPA-based methods, are limited in detecting point mutations and are low-throughput, leading to inaccurate results and missed diagnoses in conditions like spinal muscular atrophy, as they primarily quantify nucleotide differences in specific exons and are time-consuming.
Innovation Solution
The use of molecular inversion probes to capture and sequence genomic regions associated with diseases, allowing for high-throughput detection of copy number variations and point mutations, including those in SMN1 and SMN2 genes, thereby determining carrier status with greater accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If MLPA-based assays are used for carrier screening, then the assay can distinguish between SMN1 and SMN2 copy numbers, but the assay is time-consuming and has low throughput
Solution Approach 1:
The patent replaces the mechanical MLPA assay process with a molecular inversion probe-based sequencing system. The MIPs capture target DNA regions, which are then amplified and sequenced using automated high-throughput sequencing platforms, substituting manual or semi-automated MLPA procedures with a fully automated sequencing workflow that maintains copy number detection accuracy while dramatically increasing throughput
Solution Approach 2:
The patent changes the detection parameter from quantifying nucleotide differences in specific exons (MLPA approach) to sequencing and analyzing read counts across captured genomic regions. This parameter change enables simultaneous detection of copy number variations and point mutations while compatible with automated high-throughput sequencing systems
2Measurement precision
If MLPA-based assays focus on exon 7 nucleotide differences, then the assay can differentiate SMN1 from SMN2, but point mutations at other exons are missed
Solution Approach 1:
The patent makes the molecular inversion probe system multi-functional by designing probes that capture entire genomic regions containing multiple exons rather than focusing on a single exon. This allows the same assay to simultaneously perform SMN1/SMN2 differentiation through copy number analysis and detect point mutations through sequencing, eliminating the need for separate targeted exon analysis
Solution Approach 2:
The patent transitions from one-dimensional analysis (examining only exon 7 nucleotide differences) to multi-dimensional analysis by capturing and sequencing entire genomic regions. This dimensional expansion includes all exons within captured regions, enabling detection of mutations at any position while maintaining the ability to differentiate SMN1 from SMN2 through copy number determination
3Measurement precision
If MLPA-based assays quantify only exon 7 nucleotide differences, then the assay can determine copy number state, but the assay is relatively low-throughput and time-consuming
Solution Approach 1:
The patent performs preliminary capture of target genomic regions using molecular inversion probes before amplification and sequencing. This preliminary enrichment step concentrates the target DNA regions of interest, allowing subsequent rapid amplification and high-throughput sequencing, thereby reducing overall assay processing time while maintaining copy number state determination accuracy
Solution Approach 2:
The patent replaces the time-consuming MLPA quantification process with automated high-throughput sequencing. The sequencing platform automatically determines copy number states by analyzing read counts from captured regions, eliminating manual interpretation steps and significantly reducing assay processing time while maintaining measurement precision
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 provides sensitive and specific detection of copy number variations and point mutations, enhancing the reliability and speed of carrier screening for autosomal recessive traits like spinal muscular atrophy, enabling more accurate diagnosis and compatibility with automated high-throughput screening.
Implementation Method 1
molecular inversion probes capable of capturing DNA from at least one genomic region
Data Source
AI summary
The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.