Nucleotide Sequence Data Enrichment for Targeted Resequencing
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Solution Overview
Problem
Current nucleic acid sequencing methods, particularly in targeted resequencing, are laborious and time-consuming, leading to prolonged bioinformatics analysis and potential alignment errors.
Innovation Solution
A method that enriches nucleotide sequence data by incorporating probe data to determine an expected sequence, allowing for faster alignment by focusing searches within target regions rather than the entire genome, reducing errors and improving clinical relevance.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If targeted resequencing is used to focus sequencing on clinically relevant sections, then sequencing costs are reduced, but bioinformatics analysis becomes laborious and time-consuming
Solution Approach 1:
The patent applies preliminary action by incorporating probe data and expected sequence information into the sequencing data before the alignment process. The probe data (identifying which capture probe captured the fragment) and expected sequence (derived from the probe's known sequence) are integrated into the raw sequencing output, enabling the alignment algorithm to use this pre-provided information to guide the search process and significantly reduce computational time while maintaining accuracy.
2Productivity
If conventional alignment methods are used without probe data, then alignment can be performed, but alignment errors increase and clinical requirements are not met
Solution Approach 1:
The patent implements feedback by using the probe data and expected sequence information to guide and correct the alignment process. The alignment algorithm receives feedback from the probe data about which regions are most relevant and uses the expected sequence to verify and correct alignments, thereby reducing alignment errors and improving reliability while maintaining high productivity.
3Measurement precision
If the entire genome is searched for alignment, then comprehensive coverage is achieved, but analysis time increases significantly
Solution Approach 1:
The patent applies local quality by focusing the alignment search on specific local regions defined by the capture probes rather than the entire genome. The probe data identifies the specific genomic regions of interest, and the alignment algorithm concentrates computational resources on these localized areas, achieving comprehensive coverage of clinically relevant sections while dramatically reducing overall alignment time.
Data Source
AI summary
A sequencer device generates basic nucleotide sequence data 30 comprising probe data 34 of a capture probe in the sequencer device 10 and a determined sequence of identifiers 32 of a fragment of nucleic acids captured by the probe. The sequencer device outputs enriched nucleotide sequence data 36 that is enriched with data comprising a reference to a sequence 38 that is expected for the fragment of nucleic acids.