Experimental and bioinformatics considerations in cancer application of single cell genomics

Single cell genomics offers an unprecedented resolution to interrogate genetic heterogeneity in a patient's tumour at the intercellular level. However, the DNA yield per cell is insufficient for today's sequencing library preparation protocols. This necessitates DNA amplification which is a key source of experimental noise. We provide an evaluation of two protocols using micro-fluidics based amplification for whole exome sequencing, which is an experimental scenario commonly used in single cell genomics. The results highlight their respective biases and relative strengths in identification of single nucleotide variations. Towards this end, we introduce a workflow SoVaTSiC, which allows for quality evaluation and somatic variant identification of single cell data. As proof of concept, the framework was applied to study a lung adenocarcinoma tumour. The analysis provides insights into tumour phylogeny by identifying key mutational events in lung adenocarcinoma evolution. The consequence of this inference is supported by the histology of the tumour and demonstrates usefulness of the approach. (C) 2020 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

Automated summary

Single cell genomics allows for detailed analysis of genetic heterogeneity in tumors, but DNA amplification is often necessary due to insufficient DNA yield per cell. This study evaluated two micro-fluidics based amplification protocols for whole exome sequencing in single cell genomics and introduced a workflow for quality assessment and somatic variant identification. The framework was applied to study a lung adenocarcinoma tumor, providing insights into tumor phylogeny and demonstrating the usefulness of the approach.