This interactive training session explores the use of long read sequencing (LRS) technologies for validating engineered alleles in both cellular and embryonic genome engineering contexts. Participants will learn the principles of genome editing design, how LRS compares to traditional validation methods, and how to select the appropriate sequencing modality for different allele types and experimental materials. Who is this for? This workshop is designed for Early-career researchers and Experienced technicians

• seeking foundational knowledge in genome editing and sequencing technologies.
• aiming to refine protocols, troubleshoot workflows, and deepen data analysis skills.

This course covers topics including:

• A primer on genome editing strategies and allele design
• Protocols for sequencing and data generation
• Software tools for data analysis
• Hands-on exercises with real datasets
• Case studies from in-house and outsourced sequencing projects

Learning Outcomes:

• Understand genome editing principles and allele design strategies
• Learn the rationale for using LRS in validation workflows
• Gain confidence in interpreting sequencing data and alignment files
• Update and optimize genome editing and sequencing protocols
• Compare LRS platforms and outsourcing options
• Deepen skills in troubleshooting and data analysis using .bam files

Workshop Agenda: 1. Genome Editing Principles & Allele Design

• Overview of genome editing technologies (e.g., CRISPR/Cas9, base editing)
• Strategies for designing engineered alleles
• Design implications for validation
• Considerations for validation in cells and animals

2. Targeted Sequencing Modalities

• Why use LRS instead of Sanger?
• Overview of LRS platforms and their relevance to allele validation
• Choosing the right approach for your allele and material

3. Experimental Workflows

• Sample preparation and library construction
• Platform-specific considerations (e.g., ONT, PacBio)
• Adaptations for sample types (cell culture, founder animals, subsequent generation)

4. Step-by-Step Protocols

• Practical guidance for generating high-quality data

5. Data Analysis & Software Tools

• Principles of LRS data interpretation
• Overview of analysis software
• Guided exercises with real datasets

6. Deep Dive into Alignment Files (.bam)

• How to read and interpret .bam files
• Examples from in-house and outsourced sequencing
• Platform-specific nuances and troubleshooting