Spatial Genomics: Towards single-cell exome sequencing with spatial resolution in tissue sections

Abstract

Tumor heterogeneity is a major challenge in cancer research because heterogeneity of tumors leads to mixed results from different cancer clones present in a sample [Navin and Hicks, 2011]. These make the study of the population structure of a tumor and its progression very difficult. Nowadays, with the development of single-cell sequencing (SCS) it is possible to quantify tumor diversity at the single cell level in clinical [Baslan et al., 2012] thus allowing the study of complex cell mixes.

However, current technologies in SCS rely on separation techniques to isolate single-cells from tissue samples. These methods are labour intensive, produce low throughput and some lose spatial information within the tissue. To overcome this challenge we are developing a technique that will allow the characterization of genomic variations in tissue sections at a single-cell resolution. Specifically, in this study we attempt to establish an experimental workflow that will enable this characterization.

We created DNA libraries by hybridizing and extending DNA on a solid surface, followed by an exome capture. For DNA extension over a solid surface, we compared the performance of Klenow Fragment (3'-> 5'exo-) (KF) and Phi29 DNA polymerases by looking at the exome sequencing data. From the preliminary analysis of the resulting data, we observed that Phi29 library had a higher amplification bias due to lower diversity when compared to the KF exome library.