Genome-wide copy number profiling to detect gene amplifications in neural progenitor cells.
DNA sequence amplification occurs at defined stages during normal development in amphibians and flies and seems to be restricted in humans to drug-resistant and tumor cells only. We used array-CGH to discover copy number changes including gene amplifications and deletions during differentiation of human neural progenitor cells. Here, we describe cell culture features, DNA extraction, and comparative genomic hybridization (CGH) analysis tailored towards the identification of genomic copy number changes. Further detailed analysis of amplified chromosome regions associated with this experiment, was published by Fischer and colleagues in PLOS One in 2012 (Fischer et al., 2012). We provide detailed information on deleted chromosome regions during differentiation and give an overview on copy number changes during differentiation induction for two representative chromosome regions.
Department of Human Genetics, Saarland University, Building 60, 66421 Homburg/Saar, Germany.
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U
Fischer
Clinical Bioinformatics, Saarland University, Building E2.1, 66123 Saarbrücken, Germany.
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A
Keller
Clinical Bioinformatics, Saarland University, Building E2.1, 66123 Saarbrücken, Germany.
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C
Backes
Department of Human Genetics, Saarland University, Building 60, 66421 Homburg/Saar, Germany.
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E
Meese
Copy number variation; Neural progenitor cells; aCHG