GoTChA: Genotyping of Targeted loci with single-cell Chromatin Accessibility

Background & Unmet Need

• Somatic mutations drive cancer initiation and progression and are linked to hematopoiesis-related cardiovascular diseases, such as atherosclerosis
• Specific impact of mutations on human biology and their role in disease remain poorly understood
• Mutant cell populations often lack distinguishing cell surface features, making it challenging to identify, isolate and study them on a single cell basis
• High-throughput droplet-based approaches rely on RNA sequencing and are therefore limited by target expression levels and genomic locus of the mutation, while genomic DNA-based methods suffer from low throughput
• Unmet Need: High-throughput genotyping methods to better understand the impact of somatic mutations on gene regulation across various contexts, including in patient samples

Technology Overview

• The Technology: GoTChA (Genotyping of Targeted loci with Chromatin Accessibility) is a novel high-throughput method of single-cell genotyping from genomic DNA
• GoTChA allows identification of mutant and wild type cells at the single cell resolution, independently of gene expression and genomic position
• The comprehensive processing pipeline applies noise correction and provides accurate genotyping integrated with chromatin accessibility information
• GoTChA is compatible with other single cell technologies such as mtscATAC-seq for mitochondrial DNA genotyping and ASAP-seq for multiomic protein measurements
• PoC Data: In a PoC study, GoTChA genotyped 50–60% of cells for TP53 or JAK2 mutations with >96% accuracy
• GoTChA was also utilized to probe the therapeutic effect of ruxolitinib at the single-cell level

Technology Applications

• Study the impact of mutations on gene regulation in various contexts in human biology and disease
• Compare chromatin accessibility in mutated and wild type cells, potentially informing therapy decisions
• Can be combined with mtscATAC-seq for mitochondrial DNA genotyping and ASAP-seq for multiomic protein measurements

Technology Advantages

• High-throughput simultaneous ATAC-seq and genotyping within the same sequencing run
• Stable and consistent results due to novel noise correction and independence of target expression and genomic location
• User-friendly pipeline that processes data from raw reads to final genotyping calls and integration with ATAC-seq for individual cells