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

11. Comparative Genomic Hybridization (CGH) to Chromosomes and Arrays
Test Genomic DNA
Reference Genomic DNA
Cot-1 DNA
Ratio
Ratio
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. Comparative Genomic Hybridization (CGH) to Chromosomes and Arrays
Test Genomic DNA
Reference Genomic DNA
Cot-1 DNA
Ratio
Ratio
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. MPE600 Chromosome 1 Copy Number Profiles Measured by Chromosome and Array CGH-2
-1.5 -1
-0.5
0.5 1
1.5 2
50000
100000
150000
200000
250000
300000 kb
log2ratio

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

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

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

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