Non-random Molecular Barcodes for Ultra-rare Variant Detection
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Solution Overview
Problem
Current methods for detecting genetic alterations in non-invasive prenatal testing and cancer biomarker research face challenges due to background noise introduced during next-generation DNA sequencing, particularly in identifying ultra-rare variants and requiring complex library construction protocols.
Innovation Solution
The use of non-random oligonucleotide sequences as molecular barcodes to tag individual nucleic acid samples, allowing for more efficient library construction and improved detection of genetic alterations through bioinformatic tools that filter noise and generate consensus sequences for genetic alteration analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If next-generation DNA sequencing is used to detect genetic alterations, then comprehensive genetic information can be obtained, but background noise is introduced that reduces detection accuracy for ultra-rare variants
Solution Approach 1:
The patent segments the sequencing process by assigning unique molecular barcodes to individual DNA molecules before amplification. This allows post-sequencing separation of true genetic variants from sequencing errors by grouping reads with identical barcodes, thereby resolving the contradiction between comprehensive detection and noise reduction.
Solution Approach 2:
The patent introduces molecular barcodes as an intermediary element that tags individual DNA molecules. This intermediary allows the system to track and distinguish original molecules from amplification artifacts, enabling accurate detection of ultra-rare variants despite the noisy sequencing environment.
2Productivity
If traditional library construction protocols are used for sequencing, then standard procedures can be followed, but complex protocols increase the risk of introducing errors and reduce efficiency
Solution Approach 1:
The patent performs preliminary action by incorporating molecular barcodes during the library construction phase itself, rather than requiring separate tagging steps. This integration simplifies the overall workflow and reduces the number of manual operations, thereby improving efficiency while maintaining standard protocol compatibility.
3Ease of operation
If standard molecular barcoding is used, then tagging can be performed, but random oligonucleotide sequences may introduce additional variability and complexity in data analysis
Solution Approach 1:
The patent changes the parameter of barcode sequence selection from random to non-random, predetermined sequences. This modification reduces variability in the tagging process and simplifies data analysis by using consistent, known sequences, thereby improving ease of operation without increasing complexity.
Data Source
AI summary
Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining nucleic acid fragments from a sample from a test subject; sequencing the sequence constructs to obtain sequence reads; demultiplexing the sequence reads to a first and a second subset of sequences reads; generating a first set of consensus reads that correspond to the first nucleic acid fragment based on SMBs associated with the first subset of sequences reads; generating a second set of consensus reads that correspond to the second nucleic acid fragment based on SMBs associated with the second subset of sequences reads; and determining a presence of one or more genetic alterations for the test subject based on the two sets of consensus reads.