Study

'Targeted High Throughput Sequencing in Clinical Cancer Settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity'

Study ID Alternative Stable ID Type
EGAS00001000136 Resequencing

Study Description

"Background: Massively parallel sequencing technologies have brought an enormous increase in sequencing throughput. However, these technologies need to be further improved with regard to reproducibility and applicability to clinical samples and settings. Methods: Using identification of genetic variations in prostate cancer as an example we address three crucial challenges in the field of targeted re-sequencing: Small nucleotide variation (SNV) detection in samples of formalin-fixed paraffin embedded (FFPE) tissue material, minimal amount of input sample and sampling in view of tissue heterogeneity.Results: We show that FFPE tissue material can supplement for fresh frozen tissues for the detection of SNVs and that solution-based enrichment experiments can be accomplished with small amounts of DNA with only minimal effects on enrichment uniformity and data variance. Finally, we address the question whether the heterogeneity of a tumor is reflected by different genetic alterations, e.g. different foci of a tumor display different genomic patterns. We show that the tumor heterogeneity ... (Show More)

Study Datasets 4 datasets.

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Dataset ID Description Technology Samples
EGAD00001000033
"SNV detection from formalin fixed paraffin embedded (FFPE) samples"
Illumina Genome Analyzer II 6
EGAD00001000034
"Usage of small amounts of DNA for Illumina sequencing"
Illumina Genome Analyzer II 3
EGAD00001000035
"Single nucleotide variant detection in multiple foci of three prostate cancer tumors"
Illumina Genome Analyzer II 9
EGAD00001000036
"Copy number variant detection in multiple foci of three prostate cancer tumors"
Illumina Genome Analyzer II 9

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