Immune Repertoire Sequencing Contamination Detection
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Solution Overview
Problem
Current DNA-based assays for immune repertoire sequencing face challenges in detecting and quantifying contaminating nucleic acids, which can lead to reduced sensitivity and accuracy in diagnosing and prognosing diseases, particularly in detecting minimal residual disease in cancer patients.
Innovation Solution
A method involving the generation of clonotype profiles from tissue samples using sequencing of genetic markers to differentiate between nucleic acids from the individual of interest and contaminating nucleic acids, allowing for the determination of contamination levels and improving the limit of detection in immune repertoire assays.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If DNA-based assays are used for immune repertoire sequencing, then sensitivity and accuracy for disease diagnosis are improved, but contamination from external sources reduces the effective limit of detection
Solution Approach 1:
The patent introduces a reference sample as an intermediary element that contains known contaminant sequences. This reference sample serves as a mediator to detect and quantify contaminating nucleic acids in test samples by comparing sequence reads against the known contaminant database, thereby enabling sensitive detection while compensating for contamination effects
Solution Approach 2:
The patent implements feedback through the analysis of sequence reads from the reference sample to identify and quantify contaminant sequences. The system uses this feedback information to adjust and refine the detection process, allowing for the calculation of contamination levels and correction of measurement results in the actual test samples
2Reliability
If contamination detection methods are added to existing assays, then accuracy is improved, but device complexity increases
Solution Approach 1:
The patent merges the contamination detection function with the existing immune repertoire sequencing assay by using the same sequencing platform and sample processing workflow. The reference sample is processed alongside test samples, and both are analyzed using the same sequencing system, thereby integrating contamination detection into the existing assay without requiring separate complex instrumentation
Solution Approach 2:
The sequencing system is designed to perform multiple functions: it sequences the immune repertoire genes for disease diagnosis while simultaneously detecting contaminant sequences through the reference sample comparison. This multi-functionality allows a single assay system to provide both diagnostic and contamination detection capabilities, reducing overall system complexity
Data Source
AI summary
The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and/or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and/or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.