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Behavioral GeneticsTopic #9
Gene Identification
Why Search for Behavioral Genes?
• Gene identification would confirm genetic effects
• Identify the physiological basis of behavior; identify interventions
• Classification of behavior and behavioral disorders
• Genotype-environment interaction
“Human genetics is now at a critical juncture. The molecular methods used to identify the gens underlying rare mendelian syndromes are failing to find the numerous genes causing more common non-mendelian diseases.”
Neil J. Risch (2000, Nature, 405:200)
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
Search Methods (How?)• Linkage analysis (w/i family association) Advantages:
– Feasible to implement genome-wide (systematic & comprehensive); don’t need to have hypotheses about location or mechanism
– relative to alternatives, low false positive rate
Disadvantages– Limited power: detect genes accounting for 5% or more
of the phenotypic variance– Limited resolution: tight linkage can be millions of
bases away– Never finds the gene, rather at best identifies a region
Mendel vs. Galton, Redux?
• Mendelian– Single gene
– Rare
– Strong phenotype-genotype correlation
• Galtonian– Multiple genes
– Common (?)
– Weak phenotype-genotype correlation
Positional cloning strategy has been very successful in mapping genes that are rare and have large phenotypiceffect, even if for common disease (BRCA-1, BRAC-2, APP, MODY-1,-2,-3)
Search Methods; cont.• Allelic Association: association between
allele status and phenotype in unrelated individuals. Population-level association
Stomach Cancer
- +
O
Not O(A,B,AB)
40
40
60
60
Allelic Association
• Advantages– In principle, very high statistical power– In principle, can identify causal agent
• Disadvantages– Need functional polymorphisms in a candidate
gene– Concern about false-positives due to mis-matching
cases and controls
Ethnic Group #1:- Hyper + Hyper
O 24
(.40)
16
(.40)
40
(.40)
Not O
36 24 60
60 40 100
- Hyper
+
Hyper
O 9
(.10)
1
(.10)
10
(.10)
Not O
81 9 90
90 10 100
Ethnic Group #2:
- Hyper + Hyper
O 33
(.22)
17
(.34)
50
(.25)
Not O
117 33 150
150 50 100
Combined:
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
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
DRD4
Results
Association Studies of DRD4and Novelty Seeking
Study
Trait
N
Effect Size
Ebstein et al. (1996) Benjamin et al. (1996)
Novelty Seeking Novelty Seeking
124 315
.50*
.39*
Malhotra et al. (1996) Ebstein et al. (1997)
Novelty Seeking Novelty Seeking
193 94
-.11 .23
Jonsson et al. (1997) Vandenbergh et al. (1997)
Impulsivity Novelty Seeking
126 200
.28 not sig
Gebhardt et al. (1997) Pogue-Giele et al. (1998)
Novelty Seeking Novelty Seeking
58 281
-.14 .04
Meta-Analysis
Association Studies of DRD4 and Substance Abuse
N Phenotype Assoc.?
George et al. (1993) 72 Alcohol Yes
Adamson et al. (1995) 226 Alcohol No
Chang et al. (1997) 127 Alcohol No
Li et al. (1997) 275 Heroin Yes
Geijer et al. (1997) 139 Alcohol No
Kotler et al. (1997) 251 Heroin Yes
Why the Inconsistent Results?• False positive due to poor matching
• Low power in samples of modest size
• DRD4 effect depends on genetic background (epistasis):– Experimental studies in mouse
– APOE and AD
• False positive due to low a priori likelihood
Blum et al. (1990)
• Phenotype: Alcoholism• Genotype: A1/A2 allele at DRD2• Sample: 35 alcoholics and 35 non-alcoholics
• Finding:NotAlc Alc
A1
A2
7(20%)
28
24(69%)
11
DRD2
If real, how could the association arise?
• Linkage Disequilibrium:– Non-random association of alleles at linked loci– Can lead to population associations between
non-functional genetic markers and phenotypes
s s s SO O O A
Non-Sz, O-blood type Mother Sz, A-blood type Dad
Suppose: 1. This is the original mutation 2. Distance is = .05 3. Everyone has 4 children
S
A
A A A A
I - 100%
II - 100%
O
III - 94%
IV - 89%
V - 85%
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– Whether the mutation has been introduced
more than once
• In short, it depends on the evolutionary history of the population
Linkage Disequilibrium
Challenges of Gene Identification
“of the 166 putative associations which have been studied three or more times, only 6 have been consistently replicated.”
•Hirschhorn et al. (2002). “A comprehensive review of genetic association studies. Genetics in Medicine 4:45-61.
“detection of linkage and positional cloning of specific disease-susceptibility loci remains elusive.”
-- Altmüller et al. (2001). AJHG, 69: 936-950
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., > 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)
Therefore
• In outbred populations (e.g., the US), LD may not extend much beyond 3 kb a genome-wide LD study would require 500,000 markers !
• Founder or isolated populations may need fewer:– Small # of founders, little immigration, expansion
– Samii, Costa Rica, Quebec, Iceland, Japan
Are there other explanations for the DRD2-Alcoholism Association?
• Linkage Disequilibrium
• False positive owing to ethnic mismatching
DRD2 A1 allele frequencies
Is it really going to take genome-wide studies with 500,000 markers to map
complex diseases?• Validity of CDCV hypothesis
• Genome-wide association study of ‘functional’ SNPs (~ 60,000-100,000)
• HapMap project
Haplotypes• Allelic constitution of multiple loci on a
single chromosome
• 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
Cardon & Abecasis (2003). Using haplotype blocks to map the human genome.Trends in Genetics, 19: 135-140.
Although 9 markers in block 4, only 4 possible haplotypes, which
can be determined by only 3 markers
Linkage
Allelic Association
Linkage
Disequilibrium
Type of Association
w/i Family between
marker and phenotype
Pop assoc btw functl poly and phenotype
Pop assoc btw marker and phenotype
Interpretation
Region implicated
Gene or nearby gene
implicated
Region implicated
Genome-wide
Yes, 300-400
markers
Not now but maybe
in the future(~100,000)
Not now but maybe
in future (~500,000)
Resolution
Typically w/i 8-10
centimorgans recombination
Not relevant
Typically (much) less than 1 centimorgan
Preferred Sample
Large pedigrees
Sib pairs
Unrelated individuals
Genetic isolates
if rare
Sensitivity
Relatively low
Relatively High
Relatively High
Specificity
Relatively High
Relatively Low
Relatively High (?)