1. HANNIE KREMER
KNO & ANTROPOGENETICA

2. ANTROPOGENETICA – HUMAN GENETICS

3. Interpret DNA variation – monogenic and complex disorders
Things we do
Map diseases to chromosomes (position) - monogenic and complex disorders
Interpret DNA variation – monogenic and complex disorders
Understand the function of genes - pathogenesis
Therapy
98% Identical
99,8% identical

4. Things we do
Map diseases to chromosomes (position) - monogenic disorders
Interpret DNA variation – monogenic and complex disorders
Understand the function of genes - pathogenesis
Therapy

5. MAP DISEASES TO CHROMOSOMES
MONOGENIC DISORDERS

6. A B
Linkage:
If a gene and a marker are on the same chromosome they will segregate together
UNLESS
They are separated by recombination n * A B n *

7. A B A B * n * n B A B A * n n *

8. Robinow syndrome
Short stature
Wide-spaced eyes
Short nose
Small penis

9. Linkage interval Robinow syndroomcM
Chromosoom 9q21-q22.3
D9S1842
2.8
D9S1781
2.1
ROR2
D9S197
0.6
D9S1816
max = 6.47
 = 0
D9S1842
0.1
D9S280
1.4
D9S1851
D9S287
1.6
D9S176
Human Genetics Nijmegen

10. Robinow syndrome Ror2 null mouse
Human Genetics Nijmegen
Robinow syndrome Ror2 null mouse
From DeChiara et al. Nature Genetics March 2000

11. MAP DISEASES TO CHROMOSOMES
COMPLEX DISORDERS

12. Genotyping Single Nucleotide Polymorphisms (SNPs)
> 1 SNP per >3 kb
…cctcctagggttgcaaagcctccttggctatg…
…cctcctagggttgcatagcctccttggctatg…
Person B:
Person A:
Allel 1
Allel 2
~ 1,000,000 SNPs

13. Whole genome association studies Diabetes type 1 Obesity ADHD
500,000 SNPs
Whole genome association studies
Diabetes type 1
Obesity
ADHD
2000 cases controls
SNPs indicate genes involved
arrays
Case control design
Gene 1
Gene 2
Gene 3
Gene 4 ……
Gene

14. Whole genome association study
500,000 SNPs
Whole genome association study
Obesitas
9000 cases controls
BMI > 30
FTO gene
arrays
Case control design
Frayling et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316: , 2007.

15. Whole genome association study
SNPs
Whole genome association study
Obesitas
9000 cases controls
BMI > 30
FTO gene
arrays
35% kg
50% kg
15% kg
FTO gene

16. INTERPRET GENETIC VARIATION
Sequence variation at a specific nucleotide
Copy number variations (CNV)

17. p63 gene mutations in EEC syndrome
TA-p63 TA
SAM
DNA binding
Iso
A315E
L162P
R313G
Y163C
D312H
D312N
Ins A
Y192C (3)
C269Y
P309S
C308S
C308Y
S272N
V202M
L248C
C306R
R279C (3)
R279H (12)
R279Q
R304W (8)
R304Q (14)
R304P
R204W (10)
R204Q (7)
R204L
R227Q (8)
R280C (6)
R280H (2)
R280S
29 Mutations in 90 families
28 missense
1 frameshift

18. Structure model of p63 DNA binding domain

19. 276 copy number abnormalities in 100 patients with
Mental Retardation
How do we differentiate normal variation from causal changes?

20. Patient 1 Genomic profile obtained 250K SNP array
Log 2 Patient/Control

21. de novo inherited variation
Chromosome 1
Paient 1
Chromosome 15
Mother
Father
Chromosome 1
Chromosome 15

22. Next Generation sequencing
Alex Hoischen
Christian Gillisen
Next Generation sequencing

23. 1953
The complete genome of an individual by massively parallel DNA sequencing. Wheeler et al. Nature, April 2008
Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing

24. Nature genetics
Question of the year 2007
The sequencing of the equivalent of an entire human genome for $1,000 has been announced as a goal for the genetics community
What would you do if this sequencing capacity were available immediately?

25. Can we look at the all EXons of the genOME?
Exome sequencing!
mapped reads
formed contigs
targeted exon(s)
1.) Sequence Capture
2.) Sequencing
3.) Mapping
4.) Mutation detection

26. ABI SOLID 600 million map-able 50bp reads  30Gb
Roche million map-able 500bp reads  500Mb

27. ~10,000 non-synonymous coding variants*
* Per individual genome
~3,000,000 SNP variants*
~1,000,000 CNVs*
To understand human health and disease we have to understand all types of genomic variation:
~4,000,000 variants
~10,000 non-synonymous coding variants*

28. Focus on de novo disease
4 DNAs from patients with Schinzel-Giedion syndrome
patient samples n=14
4 human exomes: 2.5Gb output per sample

30. Alex Hoischen
Bregje van Bon
Christian Gillisen
De novo mutations of SETBP1 cause Schinzel-Giedion syndrome in 13 patients
Alexander Hoischen*, Bregje WM van Bon*, Christian Gilissen*, Peer Arts, Bart van Lier,
Marloes Steehouwer, Petra de Vries, Rick de Reuver, Geert Mortier, Koen Devriendt, Marta
Z Amorim, Nicole Revencu, Alexa Kidd, Mafalda Barbosa, Anne Turner, Janine Smith,
Christina Oley, Alex Henderson, Ian M Hayes, Elizabeth M Thompson, Han G Brunner,
Bert BA de Vries, Joris A Veltman
Nature Genetics

31. Things we do
Map diseases to chromosomes (position) - monogenic disorders
Interpret DNA variation – monogenic and complex disorders
Understand the function of genes - pathogenesis
Therapy

32. Photoreceptor cilium protein complex
Retinitis Pigmentosa
RPGR

33. * Photoreceptor cilium protein complex Arl3 RP2 lebercilin CC2D2A RPGR
PDE-δ
Arl3
RP2
β-tubulin
NPHP2
inversin *
lebercilin
nephrocystin-3
NPHP1
nephrocystin-1
NPHP5
IQCB1
NPHP3
CC2D2A
NPHP4
nephrocystin-4
RPGR
Dynein
RPGRIP1L
CEP290
RPGRIP1

34. * LCA RP LCA Photoreceptor cilium protein complex Senior Loken
PDE-δ
Arl3
RP2
β-tubulin
LCA
NPHP2
inversin
Nephron
- ophthisis *
Joubert
lebercilin
nephrocystin-3
NPHP1
nephrocystin-1
NPHP5
IQCB1
NPHP3
Joubert RP
CC2D2A
NPHP4
nephrocystin-4
RPGR
Dynein
RPGRIP1L
CEP290
RPGRIP1
Joubert / Meckel
LCA
LCA / Joubert / Meckel

35. GENETICA VAN GEHOORVERLIES ROL VAN BIOINFORMATICA

36. AANGEBOREN GEHOORVERLIES
~ 1 in 900 children has congenital hearing impairment >20 dB in one or more frequencies
50 % inherited
50% environmental
Ototoxic drugs
Acustic trauma
Infections
70% Nonsyndromic
30% Syndromic
Usher
Alport
Pendred
Norrie
Waardenburg
Branchio-Oto-Renal
Jervell and Lange-Nielsen
~%77 AR
~%77 AR
~%22 AD
~%22 AD
~%1
X-linked
<%1 Mitochondrial
Known Genes 6

37. Vraag van patiënt naar de oorzaak beantwoorden:
WAAROM IS HET OPHELDEREN VAN OORZAKEN
VAN ERFELIJKE ZIEKTEN BELANGRIJK?
Vraag van patiënt naar de oorzaak beantwoorden:
is het erfelijk - erfelijkheidsadvies
Vroege diagnostiek van familieleden – goede
begeleiding
Inzicht in genen/eiwitten die essentieel zijn voor
ontwikkeling en functie van het binnenoor
Handvaten voor therapie

38. FAMILIE TR57

39. DFNB63 LOCUS TR57 26 bekende of voorspelde genen ~5.29 Mb DFNB63
15.5
15.4
DFNA32
15.3
TR57
FT1A-G
PKDF702
DFNB63
FT2
1.03 Mb
15.2
15.1
USH1C
14.3
14.2
D11S2371
D11S1337
D11S4179
D11S1291
D11S916
D11S1314
D11S4139
D11S4136
D11S4113
D11S987
14.1 13
26 bekende of voorspelde genen
DFNB51 12
11.2
11.12
11.11 11
12.1
~5.29 Mb
12.2
12.3
DFNB63
13.1
FGF3
13.2
13.3
DFNB63
13.4
13.5
MYO7A
14.1
14.2
14.3 21
22.1
22.2
22.3
23.1
DFNB24
23.2
23.3
TECTA
24.1
24.2
24.3 25
DFNB20

40. LRTOMT KARAKTERISATIE
Genome browser build 36.1
LRTOMT1
LRTOMT2

41. EFFECT VAN MUTATIES Catechol-O-methyltransferase domein
A215A
G163VfsX4 (c.358+4G>A)
3’ UTR
E110K
A29SfsX54 (c.358+4G>A)
W105R
R81Q
Catechol-O-methyltransferase domein

42. MOLECULAR MODELING

43. EFFECT VAN MISSENSE MUTATIES

44. HET BINNENOOR

45. SAMENVATTING Bioinformatica is essentieel voor verschillende
stappen in studies naar ziektegenen
De structuur en functie van het humane genoom
en genen zijn nog lang niet in kaart gebracht
De oorzaak van DFNB63 is gelegen in defecten in
het LRTOMT gen. Het precieze effect van
mutaties in dit gen op de functie van het
binnenoor is nog niet duidelijk.