Nucleic Acid Variant Calling Using Multi-Flow Sequencing Signals
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Solution Overview
Problem
Existing sequencing methods face challenges in accurately and efficiently detecting short genetic variants due to single-signal errors and the high cost and time associated with high-depth sequencing.
Innovation Solution
The method involves sequencing nucleic acid molecules using non-terminating nucleotides in separate nucleotide flows according to a flow-cycle order, generating test sequencing data sets with flow signals at specific positions, and determining match scores to accurately call the presence or absence of short genetic variants.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If high depth sequencing is used to overcome single-signal errors, then measurement precision is improved, but cost and time increase
Solution Approach 1:
The patent segments the sequencing process into multiple flows, where each flow sequences a subset of nucleotides. By dividing the sequencing task across multiple flows rather than relying on a single deep sequencing run, the method achieves improved measurement precision while reducing overall sequencing time and cost.
Solution Approach 2:
The patent performs preliminary actions by pre-determining the flow-cycle order and pre-assigning nucleotide flows to specific positions before sequencing. This allows for optimized variant detection without requiring excessive sequencing depth, as the flow-cycle order is designed to maximize detection accuracy from the outset.
2Measurement precision
If high depth sequencing is used to overcome single-signal errors, then measurement precision is improved, but cost increases
Solution Approach 1:
The patent segments the sequencing process into multiple flows, where each flow sequences a subset of nucleotides. By dividing the sequencing task across multiple flows rather than relying on a single deep sequencing run, the method achieves improved measurement precision while reducing overall sequencing depth requirements.
Solution Approach 2:
The patent changes the parameter of sequencing approach by introducing flow-cycle order as a controlling factor. Instead of increasing sequencing depth to improve accuracy, the method optimizes the flow-cycle order and nucleotide flow assignment to achieve high accuracy with lower sequencing depth.
3Device complexity
If single-signal sequencing is used, then device complexity is reduced, but measurement precision deteriorates
Solution Approach 1:
The patent segments the sequencing process into multiple flows with different nucleotide assignments. This segmentation allows the system to maintain relative simplicity while improving measurement precision, as each flow operates independently with well-defined parameters rather than requiring complex real-time adjustments.
Solution Approach 2:
The patent performs preliminary actions by pre-determining the flow-cycle order and pre-assigning nucleotide flows to specific positions before sequencing. This allows for optimized variant detection with simpler sequencing mechanics, as the complex optimization is performed in advance rather than during real-time sequencing.
Data Source
AI summary
Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.