Paired Immune Receptor Chain Determination via Frequency Matching
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Solution Overview
Problem
Current methods for identifying and isolating functional T cell receptors (TCRs) are cumbersome and inefficient, particularly for cancer and autoimmune disease treatment, as they require repeated processes for each patient and only provide information from single receptor chains, missing useful data from correctly paired TCRα and TCRβ chains.
Innovation Solution
A method involving partitioning a sample into subsets, determining nucleotide sequences of TCRα and TCRβ chains, and identifying paired chains based on frequency and occurrence across subsets to reconstruct functional TCRs.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If single cell analysis, cloning and receptor isolation is performed for each patient, then TCRα and TCRβ subunits can be identified, but the process is repeated for each patient and is time-consuming
Solution Approach 1:
The patent segments the TCR identification process into two independent parts: (1) high-throughput sequencing to obtain nucleotide sequences of TCRα and TCRβ chains separately, and (2) bioinformatic pairing based on frequency matching. This segmentation allows parallel processing of multiple patient samples without repeated cloning, significantly reducing time while maintaining identification accuracy through computational pairing methods.
2Productivity
If nucleotide sequences of TCRα and TCRβ chains are determined separately, then sequencing efficiency is improved, but information from correctly paired chains is lost
Solution Approach 1:
The patent implements a feedback mechanism where nucleotide sequences of TCRα and TCRβ chains are independently sequenced with high efficiency, then fed into a bioinformatic pairing algorithm that uses frequency matching to correctly associate paired chains. This feedback loop recovers the paired chain information that would otherwise be lost, enabling reconstruction of functional TCR pairs from separately sequenced subunits.
Solution Approach 2:
The patent changes the parameter of chain association from physical linkage (in intact TCR molecules) to statistical correlation (frequency matching of nucleotide sequences). By sequencing TCRα and TCRβ chains separately and identifying paired chains through matching occurrence frequencies across multiple sequences, the method maintains productivity while recovering paired chain information through parameter transformation.
3Reliability
If current methods are used for TCR identification, then functional TCRs can be isolated, but the methods are cumbersome and inefficient for cancer and autoimmune disease treatment
Solution Approach 1:
The patent replaces the mechanical and manual processes of single cell analysis, cloning, and physical isolation with a bioinformatic system. Nucleotide sequences are obtained through high-throughput sequencing, and paired TCR chains are identified computationally using frequency matching algorithms. This substitution eliminates cumbersome manual operations while maintaining reliable isolation of functional TCRs, significantly simplifying the overall process for cancer and autoimmune disease applications.
Data Source
AI summary
The invention is directed to methods for determining nucleic acids that encode immune receptor chains originating from the same cell, that is, paired immune receptor chains. Methods of the invention comprise high-throughput sequencing of rearranged nucleic acids encoding immune receptors from one or more samples of lymphocytes. In one aspect, from a plurality of subsets of a sample, nucleic acids encoding separate chains of a pair are separately sequenced, wherein the size of the sample and the number of subsets are selected so that the distribution of lymphocytes approximates a binomial model. Paired chains are determined by identifying pairs that appear together or that are entirely absent in the subsets.