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Behavioral Genetics Topic

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New York Times 'there is no basis in the genetic code for race' Craig Ventner ... defined as one of a group of populations constituting the species Homo sapiens ... – PowerPoint PPT presentation

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Title: Behavioral Genetics Topic


1
Behavioral Genetics Topic 9
  • Gene Identification

2
Glazier, A.M. et al. (2002). Science, 298
2345-2349.
3
Mendel vs. Galton, Redux?
  • Galtonian
  • Multiple genes
  • Common (?)
  • Weak phenotype-genotype correlation
  • Mendelian
  • Single gene
  • Rare
  • Strong phenotype-genotype correlation

Positional cloning strategy has been very
successful in mapping genes that are rare and
have large phenotypic effect, even if for common
disease (BRCA-1, BRCA-2, APP, MODY-1,-2,-3)
4
Search Strategies (Where?)
  • Non-targeted
  • genome-wide
  • Targeted
  • Chromosomal anomaly (e.g., partial trisomy 5 and
    SZ, VCFS)
  • Biological-based hypotheses (e.g., DRD4 and
    Novelty-seeking)
  • Animal models
  • Positive linkage result from a non-targeted
    search
  • Micro-array findings

5
Search Methods (How?)
  • Linkage analysis (w/i family association)
  • Advantages
  • Feasible to implement genome-wide (systematic
    comprehensive) dont need to have hypotheses
    about location or mechanism
  • As compared to alternatives, relatively low false
    positive rate
  • Disadvantages
  • Requires family-study design
  • Good for genes of large effect low power to
    detect genes accounting for 5 or less of
    variance
  • Limited resolution tight linkage can be millions
    of bases away
  • Never finds the gene, rather at best identifies a
    region

6
Search Methods cont.
  • Allelic Association association between allele
    status and phenotype in unrelated individuals.
    Population-level association

Stomach Cancer
-

O
40
60
Not O (A,B,AB)
40
60
7
Allelic Association
  • Advantages
  • Easy design to implement
  • In principle, very high statistical power
  • In principle, can identify causal agent
  • Disadvantages
  • Need to know functional polymorphisms in a
    candidate gene
  • Concern about false-positives due to mis-matching
    cases and controls

8
Ethnic Group 2
Ethnic Group 1
Combined
9
The Confounding Role of Ethnicity
  • In candidate gene studies, if
  • The phenotype (disorder) varies as a function of
    ethnicity
  • The genetic polymorphism varies in frequency as a
    function of ethnicity
  • Then,
  • An artifactual association between genetic
    polymorphism and disorder can be observed

10
Ebstein et al. (1996)
  • Phenotype Personality trait of novelty-seeking
  • Sample 124 young Israelis
  • Genotype Variable 48 base repeat sequence in
    Dopamine D4 Receptor gene (DRD4)
  • Finding 7 repeat allele associated with higher
    novelty seeking

11
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12
Results
13
Association Studies of DRD4 and Novelty Seeking
14
Association Studies of DRD4 and Substance Abuse
15
Meta-analysis of DRD4 and Impulsive Personality
Munafo, M.R. et al. (2008). Biological
Psychiatry, 63 197-206.
16
Why the Inconsistent Results?
  • False positive due to poor matching
  • Low power in samples of modest size
  • DRD4 effect depends on genetic background
    (epistasis)
  • APOE and AD
  • DRD4 effect may depend on environmental context
  • DRD4 association may be indirect

17
Blum et al. (1990)
  • Phenotype Alcoholism
  • Genotype A1/A2 allele at DRD2
  • Sample 35 alcoholics and 35 non-alcoholics
  • Finding

Not Alc
Alc
7 (20)
24 (69)
A1
A2
11
28
18
Winners Curse
Cumulative Odds Ratio as a Function of
Publication Year
Original OR8.7
Final OR1.4
Smith et al. (2008) American Journal of
Epidemiology, 167(2) 125-138.
19
DRD2
20
If real, how could the association arise?
  • Linkage Disequilibrium
  • Non-random association of alleles at linked loci
  • Can lead to population (indirect) associations
    between non-functional genetic markers and
    phenotypes

21
Non-Sz, O-blood type Mother
Sz, A-blood type Dad
s
s
s
S
O
O
O
A
Suppose 1. This is the original mutation
2. Distance is q .05 3.
Everyone has 4 children
22
I - 100
S
A
II - 100
A
A
A
A
III - 94
O
IV - 89
V - 85
23
Linkage Disequilibrium Mapping
  • Linkage disequilibrium will be a function of
  • How tightly linked the two loci are
  • The number of generations since introduction of
    the original mutational event
  • In short, it depends on the evolutionary history
    of the population

24
Linkage Disequilibrium
25
Common Disease-Common Variant (CDCV) Hypothesis
  • The heritable basis of common, complex disease
    owe primarily to alleles that are
  • Relatively common (i.e., not rare, e.g., gt 10)
  • Experience little selective pressure (i.e., only
    disadvantageous when combined with other
    mutations)
  • Ancient (i.e., introduced more than 5000 Gs or
    100,000 yrs ago)

26
Therefore
  • In outbred populations (e.g., the US), LD may not
    extend much beyond 3 - 6 kb ? a genome-wide LD
    study would require 500,000 - 1,000,000 markers!
  • Founder or isolated populations may need fewer
  • Small of founders, little immigration,
    expansion
  • Samii, Costa Rica, Quebec, Iceland, Japan

27
Are there other explanations for the
DRD2-Alcoholism Association?
  • Linkage Disequilibrium
  • False positive owing to ethnic mismatching

28
DRD2 A1 allele frequencies
29
Genome-Wide Association A Matter of Numbers
  • There are 11,000,000 SNPs in the Human Genome
  • Strategies
  • One polymorphism for every gene 20,000 SNPs
  • Polymorphisms that change coding sequence 60,000
    SNPs
  • Every 3,000 to 6,000 bases 500,000 to 1,000,000
    SNPs
  • Take advantage of the haplotype structure of the
    genome

30
Carlson, C.S. (2004). Mapping complex disease
loci in whole-genome association studies. Nature,
429 446-452.
31
Haplotypes
  • Haplotype is a generalization of the concept of
    genotype to multiple loci
  • Recombination is not random, but rather there are
    recombination hot spots
  • This gives rise to blocks of DNA (haplotypes)
    where there is very little recombination w/i
    blocks but strong recombination between blocks

32
Haplotypes
  • 3 Genotypes
  • AT at locus 1
  • CG at locus 2
  • GC at locus 3
  • Haplotypes (alleles inherited together on same
    chromosome)
  • ACG TGC

A
T
C
G
G
C
33
Although 9 markers in block 4, only 4 possible
haplotypes, which can be determined by only 2
markers
Cardon Abecasis (2003). Using haplotype blocks
to map the human genome. Trends in Genetics, 19
135-140.
34
Back to COMT
  • Support for a direct (i.e., causal) association
  • The polymorphism is functional
  • Allelic association studies
  • Suggestion that it may be an indirect
    association
  • Inconsistent association
  • a priori might expect Met allele would be
    high-risk
  • Shifman et al. (2002) paper

35
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36
Genetics and Race
37
Why Are Geneticists Interested in
Ethnicity/Race?
  • Disease frequencies vary as a function of
    self-identified race
  • Allele frequencies vary as a function of
    self-identified race
  • Therefore
  • Race needs to be controlled for in genetic
    studies
  • Race may provide insights into the origins of
    disease
  • Race is also a difficult topic
  • Given the history of genetics
  • To define

38
Social Construction
  • Race was used in an attempt to classify humans
    into discrete, natural groups
  • Africans
  • Americans
  • Asians
  • Caucasians
  • Oceanians
  • Racism involved imbuing these classifications
    with behavioral and hierarchical attributes

39
Biologically Meaningless
  • Researchers have unanimously declared there is
    only one race the human race
  • New York Times
  • there is no basis in the genetic code for race
  • Craig Ventner

40
What Does Biologically Meaningless Mean?
  • Current genetic data refute the notion that
    races are genetically distinct human populations.
    There are no gene variants that are present in
    all individuals of one population group and in no
    individuals of another.
  • Bonham, V.L. et al. (2005). American
    Psychologist, 60 9-15.

41
Out of Africa
42
UNESCO (1950)
  • A race, from a biological standpoint, may
    therefore be defined as one of a group of
    populations constituting the species Homo sapiens
    ... by virtue of the isolating barriers which in
    the past kept them more or less separated,
    exhibit certain physical differences ...

43
Bamshad et al. (2004). Deconstructing the
relationship between genetics and race. Nature
Reviews Genetics 5 (8) 598-608.
44
Can we Find a Better Term Than Race?
  • Ethnicity
  • Emphasizes the cultural, socioeconomic, and
    ideological differences among human groups
  • Ancestry
  • Defined geographically (Asian, sub-Saharan
    African) or geopolitically (Irish, Vietnamese),
    or culturally (Brahmin, Apache)

45
Genetic variability among groups?
  • Variants present in some but not all groups.
    There are few examples
  • ALDH2 and alcoholism
  • Variants present in all groups but at different
    frequencies. There are many examples
  • 825T allele of GNB3 ? obesity hypertension
  • (80 AA, 45 Asians, 30 European)
  • KCNJ11 ? diabetes
  • (20 African, 40 European)
  • Majority of drug response genes

46
Goldstein Hirschhorn (2004). In genetic control
of disease, does 'race' matter? Nature Genetics
36 1243-1244.
47
Race-Based Medicine?
  • Ashkenazi Jewish Genetic Panel
  • The Thrifty Genotype Hypothesis
  • General Health Disparities
  • Moderate (but not heavy) smoking more strongly
    associated with lung cancer in African-Americans
    than European or Asian-Americans

48
 
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