Optimizing the NGS pipeline in hematopoietic disease research with automated liquid handling

Cimeio Therapeutics is an applied gene editing and immunotherapy company developing a portfolio of Shielded-Cell & Immunotherapy Pairs™ (SCIP). Gene editing is used to introduce single nucleotide exchanges into target genes in hematopoietic stem cells. While the receptors of the target gene retain their natural function, the cells are protected from the paired immunotherapeutic agent. By transplanting hematopoietic stem cells, patients can rebuild their immune system with the shielded cells while the diseased cells are killed. This approach also allows the use of universally expressed targets such as CD45 and CD117, expanding the pool of patients with hematologic diseases eligible for stem cell transplantation. To evaluate potential targets, explore new variants and optimize gene editing tools, Cimeio relies on flow cytometry and next generation sequencing (NGS) to determine editing accuracy, efficiency and shielding at both the cellular and genetic level. In addition to the desired genetic editing, Cimeio also assesses for the presence of potential unwanted off-target edits. Cimeio's molecular shielding is achieved by the exchange of single nucleotides, therefore high quality sequencing data and careful set-up of the NGS pipeline are required. The ASSIST PLUS pipetting robot from INTEGRA Biosciences has been integrated into the NGS workflow and has contributed to a more consistent, less time-consuming and less error-prone set-up. Since the introduction of this liquid handling system in critical steps such as quantification and pooling of large sample numbers, an improvement in the overall quality of processing and a reduction in human-induced errors has been observed.

 

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