search query: @keyword cancer / total: 6
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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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