The neuroblastoma genome Studies of genomic alterations using copy number microarray analyzes
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The neuroblastoma genome Studies of genomic alterations using copy number microarray analyzes
Tommy Martinsson
Department of Clinical Genetics Sahlgrenska University Hospital University of GothenburgGothenburg, Sweden
NBCNS meeting - Solbacka Sept 19, 2008
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Normal ctrl.
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NBL case
1p deletionMYCN
amplification
17q gain
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1p deletion in two NBL cases
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MYCN ALK
Three NBL cases with MYCN amplification
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For more information on our NBL arrayCGH data set, see recent publication:
Carén et al., BMC Genomics. 2008 9:353.
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Three NBL cases:NMA + few additional structural changes
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Three NBL cases:No structural aberrations - only numerical changes
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A few omitted slides
- data will be submitted for publication soon
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SNP arrays enable us to …
Comparison with ”classic”
aCGH
1. Measure the gene dosage for each SNP locus 2. Identifes the genotype call for each of e.g. 250k SNP loci -
A/A A/B B/B
Given 1 and 2 ; differences in allele intensity can be estimated -
e.g. more detailed detection of loss A/- B/- - allelic imbalance e.g. A/A/B
- copy neutral LOH N: A/B T: A/A -
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Copy neutral LOH in chromosome 14 in NBL cell line SK-N-SH
CN-LOHLOH
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NBL case
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LOH LOH1 11
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Comparison
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Acknowledgements
• Helena Carén• Hannah Kryh• Linda Olsson• Jennie Erichsen• Rose-Marie Sjöberg• Cecilia Krona• Katarina Ejeskär• Susanne Fransson• Frida Abel• Catarina Darnfors• Ylva Oleskog• Maria Nethander• Staffan Nilsson
• Jonas Abrahamsson• Per Kogner