9978 – GoTChA: Genotyping of Targeted loci with single-cell Chromatin Accessibility

  • GoTChA (Genotyping of Targeted loci with Chromatin Accessibility) is a novel high-throughput method of single-cell genotyping from genomic DNA

Abstract

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

Publications

  • Myers et al. “High Throughput Single-Cell Simultaneous Genotyping and Chromatin Accessibility Reveals Genotype to Phenotype Relationship in Human Myeloproliferation.” Blood. 2021.

Patents

  • Provisional Filed

Contact Information

Name: Jamie Brisbois

Email: jrb469@cornell.edu

Phone: 646-962-7049