The neuroblastoma genome Studies of genomic alterations using copy number microarray analyzes Tommy Martinsson Department of Clinical Genetics Sahlgrenska.

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Presentation transcript:

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

Affymetrix 250k NspI array App SNP positions Average spacing 1 SNP / bp Analysis using the CNAG 3.0 software ( Copy number detection in Neuroblastomas using the Affymetrix Microarray platform

Normal ctrl.

NBL case 1p deletion MYCN amplification 17q gain

1p deletion in two NBL cases

MYCNALK Three NBL cases with MYCN amplification

For more information on our NBL arrayCGH data set, see recent publication: Carén et al., BMC Genomics :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-LOH LOH

NBL case

LOH 111

NBL case LOH 111 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