Complex Disease and Susceptibility

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Complex Disease and Susceptibility
Gene
Gene
Gene
Gene
Environment
Disease A
Disease B
Disease C
Multifactorial disorders
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Complex Disease and Susceptibility

• Single gene disorders
• Huntingtons
• Fragile X
• SCA1
• DMD
• Werners syndrome
• Cystic fibrosis

• Multifactorial
• Heart disease
• Cancer
• Stroke
• Asthma
• Diabetes
• Alzheimers
• Parkinsons

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• Cancer Statistics
• 68 of new cases involve individuals 60 years
  and older
• Why does cancer incidence
• increase with age?
• Cancer is the natural endpoint of a
  multicellular animal
• Balance between mutation rate and losing control

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• Genetic Mutations Leading to Cancer
• 6-hit model
• 10-7 mutations per gene per cell generation
• 1013 cells in a human
• For one cell to collect 6 mutations
• 10-42 x 1013 10-29
• Thus, 1 in 1029 chance
• Then why do we get cancer?

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• Genetic Mutations Leading to Cancer
• Multistage evolution model
• Successive mutations provide a growth advantage,
  expanding that population of mutants
• Genomic instability occurs when DNA repair
  mechanisms are mutated

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Genes altered in Cancer
Tumor Suppressors APC Axin p53 PTEN Rb TSC1,2 p1
6 INK4A
Oncogenes EGFR PDGFR ABL SRC PI3K Akt Bcl2 b-cat
enin
Genomic Stability ATM BRCA1BRCA2 BARD XPA
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p53 Guardian of the Genome
G1
M
G1/S
G2/M
S
G2
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Genes altered in Cancer
Tumor Suppressors APC Axin p53 PTEN Rb TSC1,2 p1
6 INK4A
Oncogenes EGFR PDGFR ABL SRC PI3K Akt Bcl2 b-cat
enin
Genomic Stability ATM BRCA1BRCA2 BARD XPA
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By Clark et al Part B Cropped from original Fig
1 by SLE346_B3 CC BY-SA 3.0 (http//creativecommo
ns.org/licenses/by-sa/3.0)
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Ceshi Chen, Arun K. Seth and Andrew E. Aplin
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Complex Disease and Susceptibility

• Single gene disorders
• Huntingtons
• Fragile X
• SCA1
• DMD
• Werners syndrome
• Cystic fibrosis

• Multifactorial
• Heart disease
• Cancer
• Stroke
• Asthma
• Diabetes
• Alzheimers
• Parkinsons

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Genetic Component in Complex Disorders

• Relative risk
• lr frequency in relative of affected person
• Population frequency

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Genetic Component in Complex Disorders

• Family Studies

Class of relative Proportion of genes shared Examples
First degree 50 Parent/child, siblings
Second degree 25 Grandparent/grand-child, aunt/niece
Third degree 12.5 Cousins
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Genetic Component in Complex Disorders

• Problem of environmental impact

Congenital Malformations Cleft lip Pyloric stenosis
General population 0.001 0.001
First degree relatives X40 (0.04) X10 (0.01)
Second degree relatives X7 X5
Third degree relatives X3 X1.5
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Genetic Component in Complex Disorders
Disorder Monozygotic Dizygotic
Breast cancer 6.5 5.5
Type I diabetes 30 5
Type II diabetes 50 30
Multiple sclerosis 20 6
Peptic ulcer 64 44
Rheumatoid arthritis 50 8
Tuberculosis 51 22
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Genetic Component in Complex Disorders
Disorder Monozygotic Dizygotic
Alcoholism 40 20
Autism 60 7
Schizophrenia 44 16
Alzheimers 58 26
Dyslexia 64 40
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Genetic Component in Complex Disorders

• In polygenic diseases, risk (susceptibility)
  alleles increase the phenotypic value
• Traits may appear continuously variable
• Traits may appear discontinuous

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Genetic Component in Complex Disorders

• How to find susceptibility gene?
• Four main approaches
• Candidate gene
• Parametric linkage analysis
• Non-parametric linkage analysis
• Population association studies

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Candidate gene
1

• Before searching the whole genome, think about
  what genes may be involved
• Eg., Type I diabetes
• Some genes involved in cell-mediated immunity are
  located on chromosome 6 (Human leukocyte antigen
  region)
• Linkage between Type I diabetes and HLA was
  closely examined
• After a small genomic region is isolated,
  determine best candidate gene

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Parametric Linkage Analysis
2

• Standard LOD score analysis, as used for
  single-gene disorders

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Parametric Linkage Analysis
2

• Eg., breast cancer susceptibility genes
• Collect family history of gt1500 breast cancer
  patients
• Some family histories showed multiple cases
  occurring at early ages could be a Mendelian
  allele segregating
• Best model suggested a dominant single-gene
  allele with a population frequency of 0.0006
  this suggested about 5 of total breast cancers

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Parametric Linkage Analysis
2

• Eg., breast cancer susceptibility genes
• Collect family history of gt1500 breast cancer
  patients
• Now, look for families with multiple breast
  cancer cases with early onset
• Genotype family members and look for linkage
• Linkage (significant LOD score) to breast cancer
  was found to a marker on 17q21

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Parametric Linkage Analysis
2

• Eg., breast cancer susceptibility genes
• Collect family history of gt1500 breast cancer
  patients
• The gene involved was cloned, like other
  single-gene disorders
• Breast cancer (BRCA) 1 gene tumor suppressor
  gene involved in genomic stability
• LOH leads to high penetrance of breast cancer, as
  well as ovarian cancer

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Parametric Linkage Analysis
2

• Eg., breast cancer susceptibility genes
• Collect family history of gt1500 breast cancer
  patients
• However, examination of BRCA1 mutations outside
  of affected families suggests lower penetrance

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Parametric Linkage Analysis
2

• Other successes in finding Mendelian risk factors
  in polygenic diseases
• HNPCC non-polyposis colon cancer
• MSH1, MLH1, PMS1, PMS2
• FAP familial polyposis colon cancer
• APC
• Premature heart disease - hypercholesterolemia
• Mutation of the LDL receptor

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Parametric Linkage Analysis
2

• Familial hypercholesterolemia
• Autosomal dominant

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Parametric Linkage Analysis
2

• Familial hypercholesterolemia
• 200 mg/dl - 350 mg/dl - dietary, common
• 400 mg/dl - 600 mg/dl - heterozygous, uncommon
• gt600 mg/dl - homozygous, rare

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Parametric Linkage Analysis
2

• Familial hypercholesterolemia
• Autosomal dominant allele frequency about 1150

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Parametric Linkage Analysis
2

• Spectacular misfires as well
• Bi-polar disease (manic depression)
• Initial linkage to HRAS and INS on chromosome 11
• LOD scores of 4.08 and 2.63
• Two individuals in extended family misdiagnosed
• Lowered LOD score to 1.03 and 1.75

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Non-parametric Linkage Analysis
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• Genomic regions surrounding risk alleles will be
  inherited from a common ancestor in affected
  individuals to a greater frequency than by chance
  also called autozygosity mapping
• Search for commonly inherited regions by
  polymorphic microsatellites, SNPs, etc.
• High throughput analysis critical

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Non-parametric Linkage Analysis
3

• Common to use Affected Sib-Pairs (ASP)
• Collect genotypic data for 100s of ASP
• 300 microsatellite markers genotyped for 10cM
  coverage
• Look for significant IBD (gtchance occurrence)

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Non-parametric Linkage Analysis
3

• IBD if parental alleles differ at locus, then
  sibs that have both alleles in common are
  identical by decent
• IBS if parental alleles are not know, then we
  can only say sibs are identical by state

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Population association studies
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• Association studies are carried out on
  populations
• Look for alleles that segregate with the disease
  in a whole population
• Direct causation
• Natural selection
• Linkage disequilibrium

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Population association studies
4

• Linkage disequilibrium
• Combination of alleles at two closely linked loci
  occur more often than expected by chance from
  population frequencies
• Recombination reduces linkage disequilibrium

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Population association studies
4

• Linkage disequilibrium vs. Linkage Mapping
• Mapping is performed on families with few
  informative meiosis LD is determined on
  populations after many generations
• Mapping will show linkage over large distances
  LD is visible only over short distances

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Genetic Component in Complex Disorders

• How to find susceptibility genes?
• Four main approaches
• Candidate gene
• Parametric linkage analysis
• Non-parametric linkage analysis
• Population association studies

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Alzheimers Disease (AD)

• North America 0.1 at 60, 10 at 80, 30 at 90
• Early onset lt60
• Neurofibrillary tangles in the cerebral cortex
  and amyloid plaques in the brain
• Neuronal apoptosis occurs in the hippocampus and
  cerebral cortex memory and learning

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Alzheimers Disease (AD)

• Neurofibrillary tangles polymerized tau protein
• Amyloid plaques deposition of the b-amyloid
  protein

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Alzheimers Disease (AD)

• Apoptosis of neuronal cells
• Sometimes called Programmed cell death
• Energy-utilizing program of orderly
  self-destruction
• Organized dismantling of the cell to avoid
  autoimmune reaction

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Apoptosis
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Apoptosis

• Activation of proteases (cysteine-aspartic acid
  specific called Caspases)
• Cascade of irreversable proteolysis
• Activation of endonuclease chops up the cells
  DNA no going back now!

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Apoptosis

• Apoptosis occurs
• During development
• Removal of immunological cells
• In cells with DNA damage
• Defeated in cancer cells
• Neuronal cells maintain survival by exposure to
  neurotrophins

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Search for Susceptibility Alleles for Alzheimers
Disease

• Some clues as to causative agents of AD
• Down syndrome individuals develop clinical
  features of AD when they live gt30 years
• Suggested that chromosome 21 may be involved in
  AD
• Parametric linkage analysis located a locus on
  chromosome 21q in early-onset familial AD

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Causative genes in AD

• Amyloid precursor protein (APP) over-abundant in
  Alzheimers and Down syndrome individuals
• Amyloid precursor protein gene mapped to
  chromosome 21
• Trisomy 21 causes a over-expression of genes from
  chromsome 21, including APP

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Causative genes in AD

• APP a causative agent of AD and involved in
  pathology of Downs syndrome
• Large transmembrane protein processed by a, b or
  g-secretase
• a-secretase generates Aa40 protein non-toxic
  and the main protein in normal brain

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Causative genes in AD

• b and g-secretase generates Ab42 protein toxic
  and insoluble which forms plaques
• After APP was found by parametric linkage,
  mutations were found
• In familial AD, mutations in APP increased the
  amount of Ab42 cleavage

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Causative genes in AD

• More parametric linkage analysis within families
  of early-onset AD
• Presenilin I and II were discovered on chromosome
  14 and 2
• Presenilin I is a g-secretase leading to
  increased Ab42 secretion

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Causative genes in AD

• 1 of AD is familial, and shows strong Mendelian
  inheritance of altered Ab42 generation
• What about risk alleles in sporadic AD? 99 of
  cases

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Causative genes in AD

• Non-parametric linkage analysis was performed on
  Affected Pedigree Member (APM)
• 32 families in which 87 of 293 members showed AD
• Linkage with locus on chromosome 19

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Causative genes in AD

• In this region was the gene for Apolipoprotein E.
• ApoE was found in plaques and tangles
• Good candidate
• A population association study was performed
• Three alleles of ApoE were identified
• ApoE2 (6), ApoE3 (78) and ApoE4 (16)
• Strong LD was found for allele ApoE4 and several
  nearby SNPs

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Causative genes in AD

• ApoE4 is a risk factor Alzheimers disease

ApoE4 dose affected Relative Risk Age of onset
0 20 1 84.3
1 46.6 2.84 75.5
2 91.3 8.07 68.4
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Summary

• Family, adoption and twin studies provide
  evidence of genetic component to complex disease
• Risk of disease is the combined effect of
  polygenes influenced by environment, thus termed
  multifactorial
• Combined affect of many common alleles each
  providing a small effect, or of a few uncommon
  alleles with large effect
• Candidate gene, parametric and non-parametric
  linkage analysis, and population association
  analysis are used to find risk factors for
  multifactorial disease