UMI Redundant Read Consensus for Low-Frequency DNA Variant Detection
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Solution Overview
Problem
Next generation sequencing technologies face challenges in accurately detecting sequences of very low allele frequency due to errors and noise from sources like sample defects, PCR, library preparation, and sequencing, which hinder the detection of sequences in small quantities, such as fetal cell-free DNA and circulating tumor DNA.
Innovation Solution
The use of unique molecular indices (UMIs) on both strands of sequencing adapters, combined with physical and virtual UMIs, to identify and correct sequencing errors, allowing for accurate determination of nucleic acid fragment sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If sequencing depth is increased to detect low allele frequency sequences, then detection sensitivity is improved, but sequencing errors and noise from PCR and library preparation are also amplified
Solution Approach 1:
The patent segments the sequencing process by introducing unique molecular indices (UMIs) that act as barcodes to identify and group reads originating from the same original DNA molecule. This segmentation allows error correction within each UMI group while maintaining the ability to detect low-frequency variants across the entire sample.
Solution Approach 2:
The patent introduces UMIs as an intermediary element between the original DNA molecule and the sequencing reads. These UMIs serve as mediators that link multiple reads to their source molecule, enabling the system to distinguish between true low-frequency variants and sequencing errors without requiring increased sequencing depth.
2Reliability
If redundant reads are used to suppress sequencing errors, then sequencing accuracy is improved, but the complexity of data processing and error correction algorithms increases
Solution Approach 1:
The patent applies UMIs to DNA molecules before sequencing, creating a preliminary tagging system that simplifies subsequent error correction. By pre-grouping reads based on their UMI identifiers, the system avoids the need for complex post-sequencing analysis to determine which reads originate from the same molecule.
Solution Approach 2:
The patent uses UMIs to create simplified copies or representations of the original DNA molecule information. Each UMI acts as a compact identifier that allows the system to track and compare multiple reads without processing the entire sequence data for error correction, significantly reducing computational complexity.
3Reliability
If UMIs are applied to both strands of DNA fragments, then error suppression capability is improved, but the amount of sequencing data and processing requirements increase
Solution Approach 1:
The patent merges information from both DNA strands by applying UMIs to each strand and then combining the reads during consensus building. This merging allows error suppression through cross-validation between complementary strands while efficiently using the sequencing data without simply doubling the processing burden.
Solution Approach 2:
The patent implements a feedback mechanism where reads from both strands are compared and validated against each other during consensus sequence generation. This feedback loop allows the system to identify and correct errors by detecting inconsistencies between complementary strands, improving error suppression without requiring excessive sequencing depth.
Data Source
AI summary
The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.