Barcoded Oligonucleotide Probes for Structural Variation Mapping
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Solution Overview
Problem
Current next-generation sequencing (NGS) platforms face challenges in accurately mapping sequences with large structural variations, such as inversions and translocations, and in distinguishing clinically relevant genes from pseudogenes.
Innovation Solution
The method involves hybridizing interposing oligonucleotide barcodes to sample polynucleotides, extending the barcodes, and ligating them to create tagged complements, which are then amplified and sequenced.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If current NGS platforms are used for sequencing, then high-throughput and cost reduction are achieved, but mapping accuracy for sequences with large structural variations deteriorates
Solution Approach 1:
The patent introduces long-range linkage information as an intermediary element that connects distant genomic regions. This linkage information acts as a mediator that bridges the gap between short NGS reads and large structural variations, enabling accurate mapping by providing contextual information about the spatial relationships between genomic elements that exceed the read length limitations of current NGS platforms.
2Productivity
If current NGS platforms are used for sequencing, then high-throughput and cost reduction are achieved, but ability to distinguish clinically relevant genes from pseudogenes deteriorates
Solution Approach 1:
The patent employs long-range linkage information as an intermediary to disambiguate between clinically relevant genes and pseudogenes. This linkage information provides contextual evidence about the true genomic location and structure, allowing the system to correctly identify functional genes even when short reads alone are ambiguous due to similarity between genes and pseudogenes.
3Measurement precision
If longer read lengths are used to improve mapping accuracy, then structural variation detection improves, but sequencing cost and complexity increase
Solution Approach 1:
The patent segments the sequencing problem into two complementary components: short NGS reads for high-throughput base-level sequencing and long-range linkage information for structural context. This segmentation allows each component to operate in its optimal regime—short reads provide comprehensive coverage at low cost while the long-range information provides the structural framework needed for accurate mapping, avoiding the need for entirely complex long-read sequencing systems.
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 enhances the ability to accurately map sequences with structural variations and distinguish between clinically relevant genes and pseudogenes, improving the resolution of NGS technologies.
Implementation Method 1
a second stem region including a sequence complementary to the first stem region, wherein the second stem region is capable of hybridizing to the first stem region under hybridization conditions
Implementation Method 2
extending the 3' ends of the second hybridization pads with one or more polymerases to create extension products
Implementation Method 3
ligating adjacent ends of extension products hybridized to the same sample polynucleotide thereby making integrated strands comprising complements of the plurality of sample polynucleotides tagged with a plurality of interposing oligonucleotide barcodes
Data Source
AI summary
Provided herein are methods of detecting polynucleotides with a set of barcoded oligonucleotide probes.