Barcoded Nucleic Acid Screening for Cell Phenotype Genotype Association
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
High-throughput screening of genetic variants for phenotypes and genotypes in cell populations is challenging due to the difficulty in identifying and distinguishing between numerous genetic variations, especially as the number of variants increases, making it impractical to measure image-based phenotypes effectively.
Innovation Solution
A method involving the introduction of nucleic acids with identification and expression portions into cells, followed by imaging and sequential exposure to nucleic acid probes to determine phenotypes and genotypes, utilizing techniques like FISH, smFISH, and MERFISH for high-content optical measurements.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If cell sorting methods are used to measure fluorescence intensities for each genetic variant, then fluorescence measurement capability is improved, but the ability to associate genetic variants with general image-based phenotypes remains difficult
Solution Approach 1:
The patent introduces barcoded nucleic acids as an intermediary element that links genetic variants to phenotypic data. Each barcode serves as a unique identifier that can be detected alongside phenotypic measurements, enabling association without complex cell sorting. The barcode acts as a mediator that carries genetic variant information through the imaging process.
Solution Approach 2:
The patent creates optical copies of genetic information through fluorescent barcodes that can be detected by imaging systems. Instead of physically sorting cells, the genetic variant information is copied into a detectable optical signal form that can be measured and associated with phenotypic data in the same cell population.
2Measurement precision
If each genetic variant is characterized in isolation in many well chambers, then measurement accuracy is improved, but the approach becomes impractical as the number of variants increases
Solution Approach 1:
The patent merges multiple genetic variants into a single pooled library that can be screened simultaneously. By combining barcoded nucleic acids representing different variants into one population, the system maintains measurement accuracy while dramatically increasing throughput. The barcodes enable individual variant identification even when physically mixed together.
Solution Approach 2:
The patent creates a universal screening platform that can handle multiple genetic variants using a single assay system. The barcoded nucleic acid design allows the same imaging and detection methodology to work across diverse variants, eliminating the need for variant-specific protocols while maintaining measurement quality.
3Productivity
If a pooled library of all desired variants is created simultaneously, then screening efficiency is improved, but the ability to identify which genetic variation results in which genotype becomes difficult
Solution Approach 1:
The patent uses fluorescent barcodes that emit different optical signals to represent different genetic variants. Each barcode can be distinguished by its fluorescent properties, allowing the system to maintain genotype information in a pooled library. The optical signal serves as a readable identifier that prevents loss of genotype-phenotype associations during high-throughput screening.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables the high-throughput determination of phenotypes and genotypes in large cell populations, allowing for the identification of desirable phenotypes and their corresponding genotypes, thereby facilitating the screening of genetic variant libraries with improved efficiency and accuracy.
Implementation Method 1
determining genotype of the plurality of cells by sequentially exposing the plurality of cells to nucleic acid probes, and determining binding of target sequences of the nucleic acid probes within the plurality of cells
Implementation Method 2
utilizing techniques like FISH, smFISH, and MERFISH for high-content optical measurements
Data Source
AI summary
The present invention generally relates to imaging cells, for example, to determine phenotypes and/or genotypes in populations of cells. In some aspects, cells may be analyzed, e.g., imaged, to determine their phenotype, and their genotypes may be determined by exposing the cells to nucleic acid probes, e.g., as in smFISH. MERFISH, FISH, in situ hybridization, or other suitable techniques. In some cases, the cells may be exposed to a nucleic acid comprising an identification portion, which may be used to distinguish the cells from each other. In some embodiments, the cells may be exposed to a nucleic acid comprising an expression portion, e.g. a gene, or coding region for a non-translated RNA, etc., that when expressed, produces a protein, RNA, DNA, or the like that may alter the phenotype of the cell or the variable nucleic acid sequence can consist of promoters, gene regulatory elements, transcription factor binding sites, Cas9 guide RNA coding regions, etc. that otherwise alter the phenotype of the cell. In some embodiments, the modifications that contain either the identification portion, the expression portion, or both may be introduced into the genome of a host organism or as exogenous materials, e.g. plasmids. Such changes may involve the addition of synthetic materials, such as synthetic nucleic acids, or modifications, e.g. deletions or mutations, of the genomic material of the host organism. Other aspects are generally directed to compositions or devices for use in such methods, kits for use in such methods, or the like.