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HANNIE KREMER KNO & ANTROPOGENETICA. ANTROPOGENETICA – HUMAN GENETICS.
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Transcript of HANNIE KREMER KNO & ANTROPOGENETICA. ANTROPOGENETICA – HUMAN GENETICS.
HANNIE KREMER
KNO & ANTROPOGENETICA
ANTROPOGENETICA – HUMAN GENETICS
Things we do
1. Map diseases to chromosomes (position) - monogenic and complex disorders
2. Interpret DNA variation – monogenic and complex disorders
3. Understand the function of genes - pathogenesis
4. Therapy98% Identical 99,8% identical
Things we do
1. Map diseases to chromosomes (position) - monogenic disorders
2. Interpret DNA variation – monogenic and complex disorders
3. Understand the function of genes - pathogenesis
4. Therapy
MAP DISEASES TO CHROMOSOMES
MONOGENIC DISORDERS
A
n*
B
n
B
*
Linkage:
If a gene and a marker are on the same chromosome they will segregate together
UNLESS
They are separated by recombination
A
A
n*
B A
n*
B
A
* n
B B
n*
A
Robinow syndrome
Short stature
Wide-spaced eyes
Short nose
Small penis
Human Genetics Nijmegen
max = 6.47 = 0D9S1842
Chromosoom 9q21-q22.3D9S1842
D9S1781
D9S197
D9S1816
D9S280
D9S1851
D9S287
D9S176
2.8
ROR2
1.6
0
1.4
0.1
0.6
2.1
cM
Linkage interval Robinow syndroom
Human Genetics Nijmegen
Robinow syndrome Ror2 null mouse
From DeChiara et al. Nature Genetics March 2000
COMPLEX DISORDERS
MAP DISEASES TO CHROMOSOMES
Genotyping Single Nucleotide Polymorphisms (SNPs)
…cctcctagggttgcaaagcctccttggctatg……cctcctagggttgcatagcctccttggctatg…
Person B:Person A: …cctcctagggttgcatagcctccttggctatg……cctcctagggttgcatagcctccttggctatg…
Allel 1
Allel 2
~ 1,000,000 SNPs
> 1 SNP per >3 kb
500,000 SNPs
arrays
Whole genome association studies
Diabetes type 1
Obesity
ADHD
2000 cases 4000 controls
SNPs indicate genes involved
Gene 1
Gene 2
Gene 3
Gene 4
……
Gene 30.000
Case control design
500,000 SNPs
arrays
Whole genome association study
Obesitas
9000 cases 30000 controls
BMI > 30
FTO gene
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: 889-894, 2007.
35% +0 kg
50% +1.5 kg
15% +3.0 kg
FTO gene
500.000 SNPs
arrays
Whole genome association study
Obesitas9000 cases 30000 controls
BMI > 30
FTO gene
INTERPRET GENETIC VARIATION
• Sequence variation at a specific nucleotide• Copy number variations (CNV)
Ins A
p63 gene mutations in EEC syndrome
V202M S272N
R279C (3)R279H (12)R279Q
C306R
R304W (8)R304Q (14)R304P
R204W (10)R204Q (7)R204L R280C (6)
R280H (2)R280S
R227Q (8)
C308SC308Y
P309S
D312HD312N
C269Y
TA SAMDNA binding IsoTA-p63
Y192C (3)
L162P
Y163C
29 Mutations in 90 families28 missense1 frameshift
A315ER313G
L248C
Structure model of p63 DNA binding domain
276 copy number abnormalities in 100 patients with Mental Retardation
3
20
23 23
21
5
1
3
0
1
0
5
10
15
20
25
Pe
rce
nta
ge
of
pa
tie
nts
0 1 2 3 4 5 6 7 8 90
5
10
15
20
25
0 1 2 3 4 5 6 7 8 90
5
10
15
20
25
DNA copy number alterations identified per patient
0 1 2 3 4 5 6 7 8 9
How do we differentiate normal variation from causal changes?
Patient 1
Genomic profile obtained 250K SNP array
Log
2 Pa
tient
/Con
trol
Chromosome 15
Chromosome 15
Mother
Father Chromosome 1
Chromosome 1
Chromosome 1
Paient 1 Chromosome 15
de novo inherited variation
Alex Hoischen Christian Gillisen
Next Generation sequencing
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
1953
Question of the year 2007
Nature genetics
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?
1.) Sequence Capture
2.) Sequencing
3.) Mapping
mapped reads
formed contigstargeted exon(s)
4.) Mutation detection
Can we look at the all EXons of the genOME?EXOME sequencing!
ABI SOLID 600 million map-able 50bp reads 30Gb
Roche 454 1 million map-able 500bp reads 500Mb
To understand human health and disease we have to understand all
types of genomic variation:
~4,000,000 variants
~3,000,000 SNP variants*
~10,000 non-synonymous coding variants*
~1,000,000 CNVs*
* Per individual genome
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
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, MartaZ 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 VeltmanNature Genetics
Alex Hoischen Christian GillisenBregje van Bon
Things we do
1. Map diseases to chromosomes (position) - monogenic disorders
2. Interpret DNA variation – monogenic and complex disorders
3. Understand the function of genes - pathogenesis
4. Therapy
RPGR
Photoreceptor cilium protein complex
Retinitis Pigmentosa
RPGRIP1
NPHP2inversin
NPHP5IQCB1
nephrocystin-3
NPHP3
RPGRIP1L
NPHP4
nephrocystin-4
PDE-δ
Arl3 RP2 β-tubulin
NPHP1nephrocystin-1
RPGR
Photoreceptor cilium protein complex
CEP290
Dynein
lebercilin *
CC2D2A
RPGRIP1
NPHP2inversin
NPHP5IQCB1
nephrocystin-3
NPHP3
RPGRIP1L
NPHP4
nephrocystin-4
PDE-δ
Arl3 RP2 β-tubulin
NPHP1nephrocystin-1
RPGR
Photoreceptor cilium protein complex
Senior Loken
RP
LCA / Joubert / Meckel
Joubert / Meckel
CEP290
Dynein
lebercilin *LCA
LCA
Nephron
- ophthisis
CC2D2A
Joubert
Joubert
GENETICA VAN GEHOORVERLIES
ROL VAN BIOINFORMATICA
AANGEBOREN GEHOORVERLIES
~ 1 in 900 children has congenital hearing impairment >20 dB in one or more frequencies
50 % inherited 50% environmental
70% Nonsyndromic 30% Syndromic
~%77AR
~%22 AD
~%1 X-linked
<%1 Mitochondrial
• Usher• Alport• Pendred• Norrie• Waardenburg• Branchio-Oto-Renal• Jervell and Lange-
Nielsen
• Ototoxic drugs
• Acustic trauma
• Infections~%77AR
~%22 AD
Known Genes
21 6 166
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
FAMILIE TR57
DFNB63 LOCUS
TECTA
MYO7A
USH1C
DFNA32
DFNB20
DFNB24
DFNB51
DFNB63
D11S2371
D11S1337
D11S4179
D11S1291
D11S916
D11S1314
D11S4139
D11S4136
D11S4113
D11S987
~5.
29 M
b
15.515.4
15.3
15.2
15.1
14.314.214.1
13
12
11.2
11.1211.111112.112.212.3
13.113.213.3
13.413.514.114.214.32122.122.222.323.123.2
23.3
24.124.224.325
FGF3DF
NB
63TR57
26 bekende of voorspelde genen
FT1A-G PKDF702
DF
NB
63
DF
NB
63
DF
NB
63
FT2
1.03 Mb
LRTOMT KARAKTERISATIE
Genome browser build 36.1
LRTOMT1
LRTOMT2
EFFECT VAN MUTATIES
E110K
A29SfsX54 (c.358+4G>A)W105RR81Q
A215A
G163VfsX4 (c.358+4G>A)3’ UTR3’ UTR
Catechol-O-methyltransferase domein
MOLECULAR MODELING
EFFECT VAN MISSENSE MUTATIES
HET BINNENOOR
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.
