Spatially Linked Reads for Structural Variant Detection
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Solution Overview
Problem
Existing nucleic acid sequencing methods struggle to accurately map structural variants due to their size, complexity, and diverse nature, which challenges the assembly of genomic sequences and leads to errors in variant detection.
Innovation Solution
The use of complementary sequencing information, including spatial location and links between sequences, to detect structural variants by calculating metrics for spatially linked read pairs in both background and target regions, allowing for the identification of candidate structural variants.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If traditional shotgun sequencing methods are used to sequence large genomic DNA fragments, then the sequencing process becomes computationally intensive and time-consuming, but the connectivity and proximity information of sequence fragments is lost
Solution Approach 1:
The patent applies preliminary action by performing in-situ fragmentation directly on the flowcell surface before sequencing. This preserves the spatial relationships and connectivity information of DNA fragments in advance, so that when sequencing occurs, the proximity information is already encoded in the spatial arrangement of clusters on the flowcell, eliminating the need for computationally intensive assembly to recover this information later.
2Measurement precision
If standard mapping techniques are used for structural variants, then single nucleotide variations can be detected, but structural variants spanning dozens to thousands of base pairs cannot be accurately captured
Solution Approach 1:
The patent introduces another dimension by utilizing the spatial dimension on the flowcell surface. Instead of relying solely on sequence alignment in one dimension, the method uses the two-dimensional spatial arrangement of DNA clusters on the flowcell to detect structural variants. This additional spatial dimension enables accurate detection of large structural variants that span dozens to thousands of base pairs, which cannot be captured by standard one-dimensional mapping techniques.
3Ease of operation
If sequence fragments are fragmented in solution into smaller pieces, then the fragments become amenable to next-generation sequencing, but knowledge of their connectivity and proximity in the original template is lost
Solution Approach 1:
The patent extracts the fragmentation step from the solution phase and relocates it to the solid-phase flowcell surface. By performing in-situ fragmentation directly on the flowcell, the method extracts only the necessary fragmentation function while preserving the spatial context. This allows the DNA to be fragmented into smaller pieces suitable for next-generation sequencing while maintaining the connectivity and proximity information in the spatial arrangement of resulting clusters.
Data Source
AI summary
Systems and methods are provided for detecting a structural variant using complementary sequencing information, where the complementary information includes the spatial location of the sequence and the links between sequences. A baseline metric for the distribution of links for a low probability of structural variants may be used to determine whether variations in the number or distribution of spatially linked sequences is significant and could indicate the presence of a structural variant.