SMASH Chimeric DNA Fragments for Copy Number Variation Analysis
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current next-generation sequencing technologies face limitations in resolving copy number variants due to increased read lengths not improving resolution, as most of the genome is mapped well by short reads, leading to inefficient detection of genomic copy number variations.
Innovation Solution
The SMASH technique breaks genomic DNA into small but mappable segments, combining them into chimeric fragments suitable for NGS libraries, using a time-efficient mapping algorithm to generate high-quality copy number data at a fraction of the cost of whole genome sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If read length is increased to improve sequencing coverage, then sequencing cost efficiency improves, but copy number analysis resolution does not improve
Solution Approach 1:
The patent applies segmentation by breaking genomic DNA into small but mappable segments (mean length ~40 bp) that can be uniquely mapped, rather than using long reads. These segmented reads are then combined into chimeric fragments of suitable lengths (300-700 bp) for NGS library construction, enabling multiple independent mappings per read while maintaining copy number analysis resolution
Solution Approach 2:
The patent implements the nested doll principle by packing multiple independent mappings within each sequencing read. The chimeric fragments contain multiple short mappable segments nested within a single read structure, allowing the system to extract multiple independent mapping signals from one read, thereby improving copy number analysis resolution without increasing read length
2Measurement precision
If total number of sequence reads per lane is increased to improve copy number determination accuracy, then sequencing cost increases, but mapping quality remains limited
Solution Approach 1:
The patent applies copying by creating multiple copies of mapping information within each read through the chimeric fragment structure. Each chimeric fragment contains multiple short segments that can independently map to the genome, effectively copying the mapping function multiple times within a single sequencing read. This increases the number of usable maps per sample without proportionally increasing sequencing cost
Data Source
Figure 1A~1F
Figure 2A~2E
Figure 3A~3C
AI summary
The present invention, SMASH (Short Multiply Aggregated Sequence Homologies), is a technique designed to pack multiple independent mappings into every read. Specifically, the invention relates to a composition comprising a first mixture of different chimeric genomic nucleic acid fragments, wherein each different fragment in the mixture comprises randomly ligated DNA segments, wherein each DNA segment in the fragment is a nucleic acid molecule at least 27 base pairs in length resulting from random fragmentation of a single genome. The invention also relates to methods for generating said composition and use of said composition to obtain genomic information, for example, copy number variation.