Single-Step Sequencing for Antibody Lead Sequence Identification
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Solution Overview
Problem
Current methods for identifying lead antibody and T cell receptor sequences are inefficient and costly, as they typically require multiple sequencing steps and often lose information from lysed cells, which can lead to incomplete data on antigen-specific cells.
Innovation Solution
A method involving a single sequencing step on a sample containing both intact and fragmented B or T cells, where nucleic acid from both cell types is analyzed together to identify paired and unpaired sequences, and homologous clusters are used to select lead sequences for expression, including the use of next-generation sequencing and oligo-tagging for accurate cell identification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If multiple sequencing steps are used to identify lead antibody sequences, then measurement precision is improved, but productivity decreases and loss of time increases
Solution Approach 1:
The patent combines multiple sequencing steps into a single sequencing reaction by pooling intact cells and lysed cells together. The method sequences both paired sequences from intact cells and unpaired sequences from lysed cells in one go, eliminating the need for separate sequencing steps while maintaining the ability to distinguish between them through bioinformatic analysis.
Solution Approach 2:
The single sequencing step serves multiple functions: it sequences paired heavy and light chain sequences from intact cells, sequences unpaired sequences from lysed cells, and generates data that can be analyzed through clustering to identify homologous sequences. This multi-functional approach replaces what would traditionally require multiple specialized sequencing steps.
2Reliability
If only intact cells are analyzed, then reliability of paired sequence identification is improved, but loss of information increases
Solution Approach 1:
The patent converts the previously harmful effect of cell lysis (which was seen as a source of contamination and data loss) into a beneficial source of additional sequence information. By including lysed cells in the sequencing, the method recovers unpaired heavy and light chain sequences that would have been discarded, expanding the pool of potential lead sequences available for drug discovery.
Solution Approach 2:
The patent introduces bioinformatic clustering analysis as an intermediary process that mediates between the mixed data from intact and lysed cells. This computational approach groups homologous sequences together, allowing the method to reliably identify paired sequences from intact cells while also incorporating unpaired sequences from lysed cells that share homology with the intact cell sequences.
3Productivity
If a single sequencing step is used, then productivity is improved, but measurement precision may worsen
Solution Approach 1:
The patent implements a feedback mechanism through bioinformatic analysis where the sequencing data is processed to identify clusters of homologous sequences. This feedback loop allows the system to distinguish between paired sequences from intact cells and unpaired sequences from lysed cells, maintaining measurement precision despite the simplified single-step approach.
Data Source
AI summary
A method for identifying lead sequences for antibody or T cell receptor expression, the method comprising providing a single sample B or T cells derived from a host, performing a single sequencing step to sequence nucleic acid from the single sample, and selecting a lead sequence for expression.