Sequencer Output Screening Using Short Genetic Signature Snippets
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Solution Overview
Problem
Current techniques are inadequate in detecting malicious genetic sequences synthesized in small fragments that can be reassembled into harmful organisms, as they rely on recognizing sequences of approximately 200 base pairs, which can be circumvented by clipping and stitching small DNA segments.
Innovation Solution
The system identifies target organism signatures by breaking sequences into short snippets, using probabilistic data structures like Bloom filters to compare benign and malicious sequences, and categorizing sequences in real-time or near-real-time by matching against a database of malicious signatures.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If current techniques use sequence recognition of approximately 200 base pairs, then detection capability is maintained for traditional threats, but detection fails against malicious sequences synthesized in small fragments that can be reassembled
Solution Approach 1:
The patent divides the detection approach into two levels: (1) breaking down malicious sequences into small oligonucleotide fragments for synthesis, and (2) using multiple short signature snippets to detect these fragments. The system segments the detection process to match the segmented nature of the threat, using many short signature matches to collectively identify a malicious sequence even when fragmented.
Solution Approach 2:
The patent transitions from traditional single-sequence detection to a multi-dimensional detection approach by using multiple short signature snippets simultaneously. Instead of relying on one long sequence match, the system uses many short matches across different dimensions (multiple snippets, multiple locations), creating a composite detection signature that is robust against fragmentation.
2Measurement precision
If the system analyzes entire genetic sequences, then detection accuracy is improved, but analysis time increases significantly
Solution Approach 1:
The patent segments the genetic sequence into many short oligonucleotide fragments and uses corresponding short signature snippets for detection. This segmentation allows parallel processing of multiple short sequences rather than analyzing one long sequence at a time, significantly reducing analysis time while maintaining detection accuracy through the cumulative evidence of multiple snippet matches.
Solution Approach 2:
The system uses partial action by detecting only specific signature snippets within the full sequence rather than analyzing the entire sequence in detail. By focusing on key discriminatory snippets that are sufficient for identification, the system achieves accurate detection without the computational burden of complete sequence analysis.
3Reliability
If laboratories examine all genetic sequences provided by customers, then synthesis of malicious organisms is prevented, but false positives increase and legitimate research is hindered
Solution Approach 1:
The patent applies local quality by using multiple short signature snippets with different specificities. Some snippets are more specific to malicious sequences while others are more general. By combining results from multiple snippets with varying specificity, the system achieves high reliability in identifying true threats while minimizing false positives that would hinder legitimate research.
Solution Approach 2:
The system uses feedback by evaluating the collective evidence from multiple signature snippet matches rather than relying on a single match. The detection algorithm integrates information from multiple snippets, adjusting the likelihood of malicious intent based on the number, location, and specificity of matches, thereby reducing false positives while maintaining high detection reliability.
Data Source
AI summary
According to an example, a method of analyzing an output of a sequencer is provided comprising identifying genetic targets, obtaining target signature snippets responsive thereto, each target signature snippet derived from a genetic sequence of the genetic targets, receiving portions of a test sequence output by a sequencer sequencing a sample in real time, determining, in real time or near-real time with the sequencer sequencing the sample, whether a target signature snippet of the target signature snippets is in at least one portion of the test sequence, determining, for each genetic target, a probability the genetic target is in the sample based on the determination of whether the target signature snippet is present in the at least one portion of the test sequence, and outputting an analysis of the sample indicating the respective probability that each genetic target is present in the sample.