Somatic variant calling
Identifying somatic variants to determine treatment impact on genes.
About the client
Cytura Therapeutics is an early-stage pharmaceutical company based in the Netherlands and is developing novel drugs that target genomic instability in cancer. For their project with BioLizard, Cytura wanted to know whether treatment of human B cells with various drug combinations induced genomic changes.
About the project
Cytura works with isolated and cultured human B cells from a human donor. These B cells are then treated with various drug combinations for a certain amount of time in two separate experiments. The company then wanted to know whether their treatments resulted in any genomic changes. We, therefore, decided to look for somatic variants in the treated samples. We also checked whether these variants were shared between the different samples and we determined the genes that were affected.
These analyses provided Cytura with actionable insight into their sequencing data and drug treatment experiment.
“We experienced the collaboration as very pleasant, professional, service and result oriented.” – Cytura
Our approach
• Analysis and quality control of the sequencing data generated by the Illumina TruSight Oncology 500 assay.
• Processing of the sequencing data.
• Somatic mutation calling through the comparison of treated and untreated samples.
• Variant annotation, i.e. linking a variant to a gene and gene structure (intron/exon) and annotating the type of variant.
• Integration and visualization of the somatic variants and analysis of the overlap of mutated genes between the different drug treatments.
Results
Several somatic variants were identified in each of the treated human B cells, compared to the untreated cells, with intron variants being the most common.
Several genes were found which contained one or more variants in all or most of the samples over both experiments.
