Overview research topics and techniques 1. clinical, biochemical and molecular studies of

1. Overview research topics and techniques 1. clinical, biochemical and molecular studies of hereditary connective tissue disorders 2. genetic studies of neurofibromatosis type I, BPES and familial breast cancer 3. genetic studies of pediatric tumors (incl neuroblastoom) and Merkel cell carcinoma, genetic study of leukaemia

2. http://www.come.to/neuroblastoma Nadine Van Roy Mireille Van Gele Jo Vandesompele Katleen De Preter Jasmien Hoebeeck Filip Pattyn Bruce Poppe Stefan Vermeulen

3. Overview research topics and techniques 1.basic technology for DNA and RNA work - biochemistry of collagen 2. karyotyping 3. FISH : detection of DNA targets in cytological preparations) one or two DNA targets • CGH (comparative genomic hybridisation) : detection of • genomic imbalances of chromosomal regions • fiber FISH : FISH on stretched chromatin fibers • FICTION : FISH combined with immunophenotyping • M-FISH (multicolor FISH) : 24 or more DNA targets

5. MYCN copy number

6. Fluorescence in situ hybridisation DNA Commercial Cot1 DNA Labeling: nick translation Mix 10ml culture Denaturation and incubation at 37°C Wash, detection and counterstain Denaturation Hybridisatie o/n

9. f

10. Tumor DNA Normaal DNA Normale metaphase Groen Fluorescentie intensiteit Rood Ratio 1.0 Normal Loss Amplified Comparative genomic hybridisation - CGH

11. Ratio Ratio Comparative Genomic Hybridization (CGH) to Chromosomes and Arrays Test Genomic DNA Reference Genomic DNA Cot-1 DNA Position on Chromosome Position on Sequence

12. Comparative genomic hybridisation - CGH

13. Comparative genomic hybridisation - CGH

14. CGH profiles for chromosomes 1, 6, 8, 15 en 17 in a neuroblastoma case

15. Ratio Ratio Comparative Genomic Hybridization (CGH) to Chromosomes and Arrays Test Genomic DNA Reference Genomic DNA Cot-1 DNA Position on Chromosome Position on Sequence

16. Low and High Resolution Arrays for the Analysis of Copy Number Changes on 20q in Breast Tumors

17. Human Array CGH with ~ 1 Mb Resolution ~2500 BACs Triplicate spots 130 mm centers 864 well plates 0.5 mg DNA Random Prime Cy3 and Cy5 16 hr Hyb. 12 mm

18. 2 1.5 1 log2ratio 0.5 0 -0.5 -1 -1.5 -2 0 50000 100000 150000 200000 250000 300000 kb MPE600 Chromosome 1 Copy Number Profiles Measured by Chromosome and Array CGH

19. Assembly of microarrays for genome-wide measurement of DNA copy number Snijders et al. Nature Genetics november , 263-264

20. Low and High Resolution Arrays for the Analysis of Copy Number Changes on 20q in Breast Tumors

21. Human Array CGH with ~ 1 Mb Resolution ~2500 BACs Triplicate spots 130 mm centers 864 well plates 0.5 mg DNA Random Prime Cy3 and Cy5 16 hr Hyb. 12 mm

22. 2 1.5 1 log2ratio 0.5 0 -0.5 -1 -1.5 -2 0 50000 100000 150000 200000 250000 300000 kb MPE600 Chromosome 1 Copy Number Profiles Measured by Chromosome and Array CGH

23. Assembly of microarrays for genome-wide measurement of DNA copy number Snijders et al. Nature Genetics november , 263-264

24. Overview research topics and techniques 'real time' quantitative PCR using SYBR I Green: quantification of gene expression laser 'capture' microdissectie (LCM): dissectie van cellen uit weefselcoupes 'suppression subtractive hybridisation (SSH): comparative gene expression analysis for two cell populations microarray-analysis: 'high throughput' gene expression analysis

25. laser 'capture' microdissectie (LCM): isolation of single cells or small islets of cells from cytological preparation

26. laser 'capture' microdissectie (LCM):

27. laser 'capture' microdissectie (LCM):

29. laser 'capture' microdissection (LCM):

30. Lab-on-Chip - Bioanalyser Agilent technologies for analysis of minute amounts of DNA, RNA or protein

35. microarrays

36. microarras

37. microarrays

38. Alizadeh et al. Nature Sestri Levante 2000