Nucleic Acid Error Suppression for Low-Burden ctDNA Detection
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current sequencing methods for detecting low-burden cancer using ctDNA are limited by high costs and error rates, particularly in whole-genome sequencing, which is necessary for accurate detection but prohibitive due to the sparsity of ctDNA in plasma samples.
Innovation Solution
Utilizing the Ultima Genomics' low-cost, high-throughput sequencing-by-synthesis platform with duplex adapters and unique molecular identifiers (UMIs) for error correction, achieving deep whole-genome sequencing with error rates as low as 2.7×10−7, enabling accurate detection of ctDNA at the parts per million range.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If whole-genome sequencing is performed at high depth to detect low-burden ctDNA, then detection sensitivity is improved, but sequencing cost increases prohibitively
Solution Approach 1:
The patent extracts and sequences only the specific genomic regions containing somatic variants identified from primary tumor sequencing, rather than performing exhaustive whole-genome sequencing. This targeted approach reduces the total number of genome equivalents required while maintaining detection sensitivity for low-burden ctDNA
Solution Approach 2:
The patent performs preliminary sequencing of primary tumor DNA to identify patient-specific somatic variant profiles before analyzing ctDNA. This pre-characterization enables focused detection of known tumor variants in circulating DNA, reducing the sequencing depth required for reliable detection compared to de novo mutation discovery
2Measurement precision
If targeted sequencing protocols are used to increase sequencing depth at targeted locations, then ctDNA detection capability is improved, but the number of available genomes for sequencing is rapidly exhausted
Solution Approach 1:
The patent applies different sequencing strategies to different genomic regions: high-depth targeted sequencing is applied only to specific loci containing known somatic variants, while other regions receive minimal or no sequencing. This localized high-quality sequencing maximizes the utility of limited genome equivalents by concentrating resources where they are most needed for detection
3Reliability
If duplex sequencing with UMI error correction is implemented, then sequencing error rate is reduced, but library preparation complexity increases
Solution Approach 1:
The patent introduces unique molecular identifiers (UMIs) as intermediary molecular tags that are ligated to DNA fragments during library preparation. These UMIs serve as mediators that enable later computational error correction by grouping reads from the same original molecule, allowing error suppression without requiring complex dual-strand duplex sequencing protocols
Data Source
AI summary
Nucleic acid error suppression is provided. In various embodiments, DNA is extracted from a collection of plasma samples. A sequence library with duplex adapters is prepared by ligating a duplex adapter having a Unique Molecule Identifier (UMI) to an end of each of a plurality of strands of the extracted DNA and amplifying the extracted DNA with a first polymerase chain reaction (PCR). A subset of the whole genome library is selected and amplified with a second PCR to increase an amount of PCR duplicates. A plurality of duplex reads is sequenced from the amplified subset aligned to a host genome and denoised based on said alignment. A variant presence is detected in at least one of the plurality of duplex reads. A signature of the variant is determined, which is compared to a collection of disease-specific variant signatures. A disease type is determined based on the comparison.