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 GothenburgGothenburg, Sweden

NBCNS meeting - Solbacka Sept 19, 2008

tommy.martinsson@gu.se

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

•We like to collaborate !

• Research• Clincal diagnostics

» Contact: tommy.martinsson@gu.se

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