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Author:Henao Diaz, Emanuela
Title:Spatial Genomics: Towards single-cell exome sequencing with spatial resolution in tissue sections
Publication type:Master's thesis
Publication year:2013
Pages:59      Language:   eng
Department/School:Perustieteiden korkeakoulu
Main subject:Informaatiotekniikka   (T-61)
Supervisor:Lundeberg, Joakim ; Lähdesmäki, Harri
Instructor:Vickovic, Sanja ; Ståhl, Patrik
OEVS:
Electronic archive copy is available via Aalto Thesis Database.
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Location:P1 Ark Aalto     | Archive
Keywords:cancer
spatial information
single-cell
genomics
exome sequencing
Abstract (eng): 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.
ED:2014-01-07
INSSI record number: 48299
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