Development of computational tools for variant calling in single-cell RNAseq

Thesis

Single-cell sequencing technologies have unsurprisingly become a favourable choice for studying key biological questions about cell heterogeneity, rare cell types or lineages. It is only cell-level resolution that allows for an accurate analysis of internal cell processes such as mutagenesis. Eventually, single-cell RNAseq could provide an explanation of mechanisms that lead to the ultimate transformation of healthy tissues into cancerous lesions. One of the main interests of my lab is Barrett’s oesophagus. It is a highly clonal disease and a likely cancer precursor. We decided to take advantage of the single-cell RNAseq technology in order to attempt to identify the tissue of origin of the disease which, despite years of research, still remains unknown. However, the range of methods for identification of mutations in single cells is very limited. In order to address that, we developed our own single-cell RNAseq variant caller. We validated it on a publicly available breast cancer dataset by achieving a reasonable intersection of our results with the output of commonly used bulk tools. Furthermore, we showed that our caller was capable of identifying expected data characteristics such as known breast cancer signatures and mutations in breast cancer genes. We then applied our method to the Barrett’s dataset to investigate connections of Barrett’s with surrounding tissues. Contrary to the previous transcriptomic analysis conducted on the same dataset and indicating a Barrett’s-oesophagus connection, our results revealed a more likely link of Barrett’s with the stomach.

Authors: Zielińska, KA

• DOI: 10.5287/ora-obzrzymgp
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: single cell rnaseq single-cell barretts mutagenesis variant calling mutations sequencing cancer bioinformatics
• Subjects: Bioinformatics; Cancer