Allelic Variant Phasing With Molecular Barcodes for Distant Loci
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Solution Overview
Problem
Existing technologies face challenges in efficiently phasing allelic variants of genetic loci, particularly those that are far apart or intronic, which hinders genetic analysis and patient stratification for allele-specific therapeutics.
Innovation Solution
A method involving the partitioning of nucleic acid samples into aliquots, generating nucleic acid polymers with varied spacing regions, and phasing allelic variants on these polymers to determine the arrangement of genetic loci on chromosomes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If traditional phasing methods are used, then phasing of closely spaced genetic loci is achieved, but phasing of loci far apart or intronic regions fails
Solution Approach 1:
The method segments the chromosomal region containing distant or intronic genetic loci into smaller manageable units by introducing molecular barcodes and using targeted amplification. This allows each segment to be analyzed independently and then reassembled to determine the phase relationship between distant loci, overcoming the limitation of traditional methods that cannot reliably phase loci far apart.
Solution Approach 2:
Molecular barcodes serve as intermediaries to link distant or intronic genetic loci that cannot be directly phased. The barcodes are introduced at known positions and used to track the co-inheritance of distant loci through amplification and sequencing, enabling phase determination without requiring direct physical proximity or linkage between the target loci.
2Adaptability or versatility
If molecular barcoding and amplification are used, then phasing of distant loci is enabled, but process complexity increases
Solution Approach 1:
The molecular barcode system serves multiple functions simultaneously: it acts as a unique identifier for tracking specific chromosomal copies, serves as a primer binding site for targeted amplification, and provides a means for library preparation and sequencing. This multi-functionality reduces the need for separate systems for each task, thereby managing complexity.
Solution Approach 2:
The method changes key parameters of the DNA molecules being analyzed by introducing synthetic molecular barcodes with specific sequence properties that differ from native DNA. These parameter changes (sequence composition, length, chemical modifications) enable the barcoded molecules to be selectively amplified, purified, and sequenced using standard techniques, managing the complexity through controlled modifications.
Data Source
AI summary
Among other things, the present disclosure pertains to methods and compositions related to phasing of allelic variants of genetic loci. Phasing of allelic variants of genetic loci on an individual patient's chromosomes is highly valuable for many purposes, including patient stratification for allele-specific therapeutics.