Synthetic Barcoding for Pooled Cell Line Screening
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Solution Overview
Problem
Current pooled screening methods for cells from different genetic backgrounds are limited by their reliance on sequencing data, which restricts the number of assays that can be performed and fail to account for non-coding variants, and are unable to conduct large-population studies without scaling challenges.
Innovation Solution
Labeling multiple cell populations with unique nucleic acid barcode sequences, combining them, and performing in situ single-cell sequencing to analyze phenotypes, while using machine learning and image alignment techniques to classify genetic backgrounds and reduce artifacts.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If pooled screening approaches use sequencing data for genotype identification, then genetic background can be identified, but the number of assays that can be performed is greatly limited
Solution Approach 1:
The patent introduces synthetic nucleic acid barcodes as an intermediary element that links genetic background information to phenotypic readouts. These barcodes serve as mediators that enable genetic identification without relying on sequencing, thus expanding assay versatility while preserving genetic background information.
Solution Approach 2:
The patent replaces the sequencing-based mechanical system with a barcode-based optical detection system. This substitution eliminates the limitations of sequencing capacity while maintaining the ability to identify genetic backgrounds, enabling a broader range of assays to be performed.
2Adaptability or versatility
If pooled screening approaches use optical barcoding with single cell line, then in situ sequencing can identify perturb gRNAs, but only a single genetic background can be utilized at a time
Solution Approach 1:
The patent segments the barcoding system into modular synthetic nucleic acid barcodes that can be independently designed and assigned to different cell lines. This segmentation allows multiple genetic backgrounds to be pooled together while maintaining unique identification for each, increasing adaptability without proportionally increasing overall system complexity.
Solution Approach 2:
The patent creates a universal barcode system that can identify multiple genetic backgrounds simultaneously. The synthetic barcodes are designed to work across different cell lines and assay types, providing multi-functionality that enables pooling of diverse genetic backgrounds without requiring separate barcoding systems for each.
3Quantity of substance
If large population studies are conducted in vitro, then population-based analysis can be performed, but scaling challenges including evaporation, temperature, and plate-wise artifacts increase
Solution Approach 1:
The patent uses synthetic nucleic acid barcodes as information copies that can be replicated across large cell populations without degradation. These barcode copies enable tracking of individual cell lineages through large-scale pooled experiments, maintaining reliability even as population size increases and allowing statistical genetics analysis across thousands of cells.
Data Source
AI summary
Provided herein are methods of pooled screening of cells from different genetic backgrounds. Also provided herein are computer-implemented methods for aligning between a first plurality of images and a second plurality of images of biological samples.