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The neuroblastoma genome Studies of genomic alterations using copy number microarray analyzes

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. tommy.martinsson@gu.se.

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The neuroblastoma genome Studies of genomic alterations using copy number microarray analyzes

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  1. The neuroblastoma genome Studies of genomic alterations using copy number microarray analyzes Tommy MartinssonDepartment of Clinical Genetics Sahlgrenska University Hospital University of Gothenburg Gothenburg, Sweden NBCNS meeting - Solbacka Sept 19, 2008 tommy.martinsson@gu.se

  2. Affymetrix 250k NspI array • App. 260.000 SNP positions • Average spacing 1 SNP / 12.000 bp • Analysis using the CNAG 3.0 • software (http://www.genome.umin.jp/) Copy number detection in Neuroblastomas using the Affymetrix Microarray platform

  3. Normal ctrl.

  4. 1p deletion MYCN amplification 17q gain NBL case

  5. 1p deletion in two NBL cases

  6. Three NBL cases with MYCN amplification MYCN ALK

  7. For more information on our NBL arrayCGH data set, see recent publication: Carén et al., BMC Genomics. 2008 9:353.

  8. Three NBL cases: NMA + few additional structural changes

  9. Three NBL cases: No structural aberrations - only numerical changes

  10. A few omitted slides - data will be submitted for publication soon

  11. SNP arrays enable us to … Comparison with ”classic” aCGH • Measure the gene dosage for each SNP locus  • 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 -

  12. Copy neutral LOH in chromosome 14 in NBL cell line SK-N-SH LOH CN-LOH

  13. NBL case 4 3 2 1

  14. NBL case 4 3 2 1

  15. NBL case 4 3 2 1 1 11 LOH LOH

  16. Comparison NBL case 4 3 2 1 1 11 LOH LOH

  17. We like to collaborate ! • Research • Clincal diagnostics • Contact: tommy.martinsson@gu.se

  18. 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

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