HANNIE KREMER KNO & ANTROPOGENETICA - PowerPoint Presentation

Slide1

HANNIE KREMER

KNO & ANTROPOGENETICA

Slide2

ANTROPOGENETICA – HUMAN GENETICS

Slide3

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

Slide4

Things we do

Map diseases to chromosomes (position) - monogenic disorders

Interpret

DNA

variation

–

monogenic

and complex disorders

Understand the function

of

genes - pathogenesis

Therapy

Slide5

MAP DISEASES TO CHROMOSOMES

MONOGENIC DISORDERS

Slide6

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

Slide7

A

n

*

B

A

n

*

B

A

*

n

B

B

n

*

A

Slide8

Robinow

syndrome

Short stature

Wide-spaced eyes

S

hort nose

Small penis

Slide9

Human Genetics Nijmegen



max = 6.47



= 0

D9S1842

Chromosoom 9q21-q22.3

D9S1842

D9S1781

D9S197

D9S1816

D9S280

D9S1851

D9S287

D9S176

2.8

ROR2

1.6

0

1.4

0.1

0.6

2.1

cM

Linkage interval

R

obinow

syndroom

Slide10

Human Genetics Nijmegen

Robinow

syndrome

Ror2

null mouse

From DeChiara et al. Nature Genetics March 2000

Slide11

COMPLEX DISORDERS

MAP DISEASES TO CHROMOSOMES

Slide12

Genotyping Single Nucleotide Polymorphisms (SNPs)

…

cctcctagggttgca

a

agcctccttggctatg

…

…

cctcctagggttgca

t

agcctccttggctatg

…

Person

B:

Person

A:

…

cctcctagggttgcat

agcctccttggctatg

…

…

cctcctagggttgca

t

agcctccttggctatg

…

Allel

1

Allel

2

~

1,000,000

SNPs

> 1 SNP per >3

kb

Slide13

500,000

SNPs

arrays

Whole

genome

association

studies

Diabetes

type 1

Obesity

ADHD

2000 cases 4000 controlsSNPs indicate genes involved

Gene 1

Gene 2

Gene 3

Gene 4

……

Gene 30.000

Case

control

design

Slide14

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.

Slide15

35%

+0 kg 50% +1.5 kg

15

% +3.0 kg

FTO gene

500.000

SNPs

arrays

Whole

genome

association

study

Obesitas

9000

cases 30000 controls

BMI > 30

FTO gene

Slide16

INTERPRET GENETIC VARIATION

Sequence variation at a

specific

nucleotide

Copy

number variations (CNV)

Slide17

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)

C308S

C308Y

P309S

D312H

D312N

C269Y

TA

SAM

DNA binding

Iso

TA-p63



Y192C (3)

L162P

Y163C

29 Mutations in 90 families

28 missense

1 frameshift

A315E

R313G

L248C

Slide18

Structure model of p63 DNA binding domain

Slide19

276 copy number abnormalities in 100 patients with

Mental Retardation

How

do we

differentiate

normal

variation

from

causal

changes

?

Slide20

Patient 1

Genomic profile obtained 250K SNP array

Log 2 Patient/Control

Slide21

Chromosome

15

Chromosome

15

Mother

Father

Chromosome

1

Chromosome

1

Chromosome

1

Paient

1

Chromosome

15

de novo

inherited variation

Slide22

Alex Hoischen

Christian Gillisen

Next

Generation

sequencing

Slide23

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

Slide24

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?

Slide25

1.) Sequence Capture

2.) Sequencing

3.) Mapping

mapped reads

formed contigs

targeted exon(s)

4.) Mutation detection

Can we look at the all

EX

ons of the gen

OME

?

Exome

sequencing!

Slide26

ABI SOLID

600 million map-able 50bp reads

 30Gb

Roche 454

1 million map-able 500bp reads

 500Mb

Slide27

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

Slide28

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

Slide29

Slide30

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

Veltman

Nature Genetics

Alex Hoischen

Christian Gillisen

Bregje van Bon

Slide31

Things we do

Map diseases to chromosomes (position) - monogenic disorders

Interpret

DNA

variation

–

monogenic

and complex disorders

Understand

the

function of genes - pathogenesis

Therapy

Slide32

RPGR

Photoreceptor cilium protein complex

Retinitis Pigmentosa

Slide33

RPGRIP1

NPHP2

inversin

NPHP5

IQCB1

nephrocystin-3

NPHP3

RPGRIP1L

NPHP4

nephrocystin-4

PDE-δ

Arl3

RP2

β-tubulin

NPHP1

nephrocystin-1

RPGR

Photoreceptor

cilium

protein

complex

CEP290

Dynein

lebercilin

*

CC2D2A

Slide34

RPGRIP1

NPHP2

inversin

NPHP5

IQCB1

nephrocystin-3

NPHP3

RPGRIP1L

NPHP4

nephrocystin-4

PDE-δ

Arl3

RP2

β-tubulin

NPHP1

nephrocystin-1

RPGR

Photoreceptor

cilium

protein

complex

Senior Loken

RP

LCA /

Joubert

/

Meckel

Joubert

/

Meckel

CEP290

Dynein

lebercilin

*

LCA

LCA

Nephron

-

ophthisis

CC2D2A

Joubert

Joubert

Slide35

GENETICA VAN GEHOORVERLIES

ROL VAN BIOINFORMATICA

Slide36

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

~%77

AR

~%22 AD

~%1

X-linked

<%1 Mitochondrial

Usher

Alport

Pendred

Norrie

Waardenburg

Branchio

-

Oto

-Renal

Jervell

and Lange-Nielsen

Ototoxic

drugs

Acustic

trauma

Infections

~%77

AR

~%22 AD

Known Genes

21 6 16

6

Slide37

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

Slide38

FAMILIE TR57

Slide39

DFNB63 LOCUS

TECTA

MYO7A

USH1C

DFNA32

DFNB20

DFNB24

DFNB51

DFNB63

D11S2371

D11S1337

D11S4179

D11S1291

D11S916

D11S1314

D11S4139

D11S4136

D11S4113

D11S987

~5.29 Mb

15.5

15.4

15.3

15.2

15.1

14.3

14.2

14.1

13

12

11.2

11.12

11.11

11

12.1

12.2

12.3

13.1

13.2

13.3

13.4

13.5

14.1

14.2

14.3

21

22.1

22.2

22.3

23.1

23.2

23.3

24.1

24.2

24.3

25

FGF3

DFNB63

TR57

26 bekende of voorspelde genen

FT1A-G

PKDF702

DFNB63

DFNB63

DFNB63

FT2

1.03 Mb

Slide40

LRTOMT

KARAKTERISATIE

Genome browser build 36.1

LRTOMT1

LRTOMT2

Slide41

EFFECT VAN MUTATIES

E110K

A29SfsX54 (c.358+4G>A)

W105R

R81Q

A215A

G163VfsX4 (c.358+4G>A)

3’ UTR

3’ UTR

Catechol-

O

-methyltransferase domein

Slide42

MOLECULAR MODELING

Slide43

EFFECT VAN MISSENSE MUTATIES

Slide44

HET BINNENOOR

Slide45

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.