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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 Gothenburg Gothenburg, Sweden. NBCNS meeting - Solbacka Sept 19, 2008. [email protected]. - PowerPoint PPT Presentation
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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
Normal ctrl.
NBL case
1p deletionMYCN
amplification
17q gain
1p deletion in two NBL cases
MYCN ALK
Three NBL cases with MYCN amplification
For more information on our NBL arrayCGH data set, see recent publication:
Carén et al., BMC Genomics. 2008 9:353.
Three NBL cases:NMA + few additional structural changes
Three NBL cases:No structural aberrations - only numerical changes
A few omitted slides
- data will be submitted for publication soon
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 -
Copy neutral LOH in chromosome 14 in NBL cell line SK-N-SH
CN-LOHLOH
2
3
4
1
NBL case
2
3
4
1
NBL case
2
3
4
1
NBL case
LOH LOH1 11
2
3
4
1
NBL case
LOH LOH1 11
Comparison
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