Genome wide association studies of complex traits in outbred and isolated populations

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• Genome wide association studies of complex traits
  in outbred and isolated populations
• CM van Duijn
• Genetic Epidemiology Unit
• Erasmus MC, Rotterdam, The Netherlands

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Topics

• To what extend do isolates differ from outbred
  populations ?
• What is the role of isolates in gene wide
  association studies ?

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Population dynamics in isolates
Founder effect
Genetic drift
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Genetic Research in Isolated Populations (GRIP)
program

• Recent genetically isolated population in the
  South-West of the Netherlands
• At least 150 founders in 1750
• Substantial population growth, with minimal new
  immigration until last decades
• Genealogical data

Rotterdam
GRIP
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Comparison of genetic variability GRIP, Iceland,
CEPH
Mean number of alleles CEPH gt Iceland gt
GRIP 10.059 gt 7.623 gt 7.240 (plt0.01)
Mean heterozygosity CEPH gt Iceland gt GRIP
0.768 gt 0.758 gt 0.757 (plt0.05)
Inbreeding
Pardo et al, Ann Hum Genet 2005
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Pedigree of the GRIP population
What is the effect of isolation on genome?
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Expected fluctuations alleles proportions by
allele frequency
P

Probability loss of allele
Probability allele proportion is gt 5P0
Probability allele proportion is gt 10P0
0



0.954

0.026

0.0001

0.615

0.02

0.001

0.01

0.0083

0

0

0

0.025

0

0

0.05

0

0

0.1

0

0

0.25

0


0

0.5

P0 Allele proportion original population
Pardo et al, Ann Hum Genet 2005
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Gene
Gene
Gene
Gene
Protein
Protein
Protein
Protein
Protein
Gene
Complex disease
Protein
Protein
Gene
Protein
Gene
Gene
Rare mutations in an outbred population
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Gene
Gene
Gene
Gene
Protein
Protein
Protein
Protein
Protein
Gene
Complex disease
Protein
Protein
Gene
Protein
Gene
Gene
Rare mutations in an isolated population
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Gene
Gene
Gene
Gene
Protein
Protein
Protein
Protein
Protein
Gene
Complex disease
Protein
Protein
Gene
Protein
Gene
Gene
Common mutations in an isolated population
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Comparison of linkage disequilibrium of recently
isolated populations

• Antioquia, Colombia ((ANT)
• Ashkenazi (ASH)
• Azores (AZO)
• Central Valley of Costa Rica (CR)
• GRIP population Netherlands (NL)
• Early settlement Finland (FIC)
• Finnish subisolate of Kuusamo (FIK)
• Finland nationwide (FIP)
• Newfoundland (NFL)
• Afrikaner (SAF)
• Province of Nuoro in Sardiana (SAR)
• Caucasian general population (CAU)

Service et al, Nature Genet 2006
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Linkage disequilibrium units (LDU) for chromosome
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Service et al, Nature Genet 2006
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To what extend do isolates differ from outbred
populations?

• Have a reduced variability for rare genetic
  variants

• May show extended linkage disequilibrium

• Are often characterised by consanguinity

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Topics

• To what extend do isolates differ from outbred
  populations ?
• What is the role of isolates in gene wide
  association studies ?

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Finding genes in isolates

• Rare variants

Became very prevalent or disappeared
Linkage is most powerful approach

• Multiple common variants

Will be found also in isolated populations
Association is most powerful approach
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Finding genes in isolates

• Rare variants with major effects

Linkage example Alzheimer disease

• Multiple common variants

Association eye colour
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Pedigree Alzheimers disease (AD)

• 111 probable late onset (75 5.3 years)
  Alzheimer patients
• 103 patients were connected based on genealogy
• Genome wide screen with 420 micro-satelilite
  markers (Perkin Elmer)

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Results genome wide screen
Liu et al, AJHG in press
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Haplotype analysis chromosome 3
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Finding genes in isolates

• From linkage to association?

• From association to linkage?

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Genome wide association analysis

• Population
• 200 distantly related individuals
• Phenotype
• Cognitive function
• Genotyping
• Affymetrix 250K SNP array
• Data Analysis
• Single SNP association Type 1 error (p) nominal
  and permutation tests

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Genome wide analysis Stroop test in 200
individuals (ERF)
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Chromosome 10 region
rs17129622 rs11185978 rs7071717 Learning
0.23 0.36 0.30 Recall 0.55
0.60 0.67 Recognition 0.48 0.60
0.71 Stroop 0.00003 0.00002 0.000005 TMT-B
0.00023 0.01 0.01 Semantic Fluency
0.10 0.05 0.04 Phonological
Fluency 0.002 0.001 0.01 Block Test
0.80 0.61 0.90 Total evidence
710-13 910-13 310-14 Adjusted p-value
0.02 0.01 0.002
CYP2C19 - CYP2C9
Liu et al, AJHG in press
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Finding genes in isolates

• Rare variants with major effects

Linkage example Alzheimer disease

• Multiple common variants

Association eye colour
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Genetics of eye color

• Co-dominant trait
• Brown dominates over green, green over blue
• Strong association for blue/nonblue eye color was
  found with three OCA2 SNPs (Duffy et al. 2007)

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OCA2 and eye colour
3-SNP haplotype was observed with a frequency of
0.905 in those with blue eyes and 0.095 in
those with brown eyes
Duffy et al, AJHG 2007, 80241-252
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GWA in 192 participants of GRIP (Affymetrix 250k)

• Significant association (p1.210-9) to the OCA2
  region at chromosome 15q13.1
• Adjusted for multiple testing by 100 genome-wide
  permutations

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Rotterdam Study

• Population-based study outbred Caucasian
  population
• 12,000 subjects aged 55 years who have been
  followed for 15 years
• Sampling DNA, RNA, serum/plasma
• Screening for major diseases and risk factors
  ever 5 years
• Genome wide association Affymetrix 500K

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GWA analysis in 481 persons of the Rotterdam study
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Linkage of OCA2 to eye color in 4 families GRIP
Family 14 LOD1.6
Family 7 LOD1.4
Family 12 LOD1.1
Family 5 LOD1.1
Overall LOD 3000 relatives 22.0
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Finding genes in isolates

• From linkage to association

• From association to linkage

• Powerful replication

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Diseases studied in GRIP
Neuropsychiatric Cardiovascular Parkinson
disease Hemochromatosis Alzheimer's disease
Diabetes type 2 Stroke/ White Matter Disease
Hypertension Multiple Sclerosis
Pre-eclampsia ADHD Fertility
PCOS Depression Atherosclerosis Anxiety Hy
perlipidemia
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Diseases studied in GRIP

• Ophthalmologic Macular degeneration
• Glaucoma
• Auto-immune Type 1 diabetes
• Bone Osteoporosis
• Osteoarthritis
• Rheumatoid arthritis
• Lung COPD
• Pharmacology Response antihypertensives

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Cardiovascular assessments
Plaques, intima media thickness, pulsewave
velocity
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Ophthalmologic studies
Age related macular degeneration
Glaucoma
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Neuropsychiatric testing
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Thanks !