NGS SEED Generation from Soft-Clipped Reads for ITD Analysis
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Solution Overview
Problem
Current NGS analysis methods face challenges in accurately analyzing internal tandem duplication (ITD) due to limitations in existing commercial analysis programs.
Innovation Solution
A method and apparatus for deriving a SEED by selecting reads with the same insertion sequence or soft-clipped bases, and using these to analyze ITD, where a SEED is defined as a region including part or all of the sequence of soft-clipped bases or insertion sequences, with adjacent sequences of 12-20 bp, to facilitate rapid and accurate ITD analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional NGS analysis methods are used, then sequencing speed and coverage are improved, but ITD detection accuracy deteriorates
Solution Approach 1:
The patent segments the read sequence into distinct functional regions: soft-clipped bases (representing ITD sequences), insertion sequences (additional repeats), and matched bases (reference sequence). This segmentation allows independent analysis of each component to accurately detect ITD while maintaining overall sequencing efficiency
Solution Approach 2:
The patent extracts and isolates the soft-clipped bases and insertion sequences from the full read sequence for specialized ITD analysis. By separating these problematic regions from the standard alignment process, the method enables accurate ITD detection without compromising the speed and coverage provided by conventional NGS analysis
2Adaptability or versatility
If commercial analysis programs are used for ITD analysis, then analysis capability is improved, but accuracy and reliability deteriorate
Solution Approach 1:
The patent applies local quality analysis by examining specific regions of the sequence with different analytical approaches: soft-clipped bases are analyzed for ITD presence, insertion sequences are counted for duplication magnitude, and matched bases are used for alignment reference. This localized analysis ensures accurate ITD detection while maintaining overall analysis capability
Solution Approach 2:
The patent performs preliminary actions during the sequencing process itself by marking soft-clipped bases and identifying insertion sequences as reads are generated. This preliminary characterization of ITD features enables accurate detection without requiring complex post-processing, thereby improving reliability while maintaining analysis capability
Data Source
AI summary
One embodiment of the present invention relates to a method comprising: acquiring information about reads for an arbitrary sequence by means of an NGS analysis method; selecting reads having the same insertion sequence from among the acquired reads on the basis of a reference sequence, and b) selecting reads having the same soft-clipped bases; and selecting, as a SEED, a region including a part or all of the sequence of the soft-clipped bases of the selected reads and the insertion sequence thereof, and thus ITD can be accurately analyzed through the selected SEED, such that diagnosis, prognosis determination and the like of diseases associated with ITD can be performed thereby.