Shackman Psyc210 Module11 NatureNurture Part2

We wish to suggest a structure for
the salt of deoxyribonucleic

acid...This structure has novel
features which are of considerable
biological interest...It has not escaped
our notice that the specific pairing we
have postulated immediately
suggests a possible copying
mechanism for the genetic material
Watson & Crick Nature 1953
we should remain unabashed about the

ultimate [goal] of genomic medicine, which
[is] to transform the health of our children
and our childrens children
Lander
Nature 2011
Plan for Today

Lecture on Nature & Nurture, Part 2
The genomics revolution
Part of the motivation is to educate
you
as citizens, taxpayers, and
healthcare consumers
Take-home critical thinking

questions
PSYC 210:
The nature & nurture of T&P, Part 2
Molecular substrates of trait-like differences with a focus on
Gene-Environment Interactions
AJ Shackman
March 2015
Conceptual Roadmap
T&P are somewhat heritable
What molecular mechanisms account for
that heritability?
T&P reflects the influence of both genetic
inheritance (nature) and the
environment/experience (nurture)
Are these separate effects (G and E) or an
interaction (G x E)?
e.g., Exposure to stress and risky genes
Conceptual Roadmap
that heritability?
Are these separate effects (G and E) or an
interaction (G x E)?
e.g., Exposure to stress and risky genes
Conceptual Roadmap
that heritability?
Are these separate and independent effects
(G and E) or an interaction (G x E)?
e.g., Risky genes AND stress exposure
DNA
Quick Genetics Primer
Genes
DNA Chromosomes
- DNA is organized into chromosomes, the vectors of
heredity
- Human cells have 23 pairs of chromosomes (46 / cell),
one pair descended from mom and one from dad
DNA Chromosomes
- DNA is organized into chromosomes, the vectors of
heredity
- Human cells have 23 pairs of chromosomes (46 / cell),
one pair descended from mom and one from dad
What about genes?
https://en.wikipedia.org/wiki/Human_genom
Genes
- Gene: a region of DNA/RNA sequence, corresponding

to a unit of inheritance or single basic instruction
(recipe)
- Human genome: ~21,000-23,000 genes
- Genes hold the information to build and maintain an
organism's cells and pass genetic traits to offspring
- Genes are transcribed to RNA and used
to code protein synthesis, e.g., build
neurons, axons, transporters, vesicles,
neurochemicals, myelin, etc.
DNA/Gene messenger RNA protein
Genes

(recipe)
- Human genome: ~22,000 protein-coding genes
Genes

(recipe)
Genes

(recipe)
What makes us
different?
Alleles = Individual Differences

- Allele: a variant of a gene (genetic polymorphism)
- Different alleles can result in different observable
phenotypic traits, such as different hair color
- Most genes do not differ across individuals; only a
single allele
- When people talk about good or bad genes, they
actually mean allele (individual differences in genetic
instructions)

phenotypic traits, such as different hair color (cf.
Weasley clan)
single allele
instructions)

Weasley clan)
single allele
instructions)

Weasley clan)
single allele
instructions)
SNPs = Individual Differences

- SNP: single nucleotide polymorphism (so, a particular
kind of allele)
- 10-30 million SNPs in humans (~10M common [>1%
frequency])
- Most common type of sequence
variation (90% total variation)
SNPs = Individual Differences

- SNP: single nucleotide polymorphism (so, a particular
kind of allele)
- ~20 million SNPs in humans (~10M common [>1%
frequency])
- Most common type of sequence
variation (90% total variation)
How might we try to discover the alleles that predict

trait-like differences in T&P (N, E, C)
or intermediate phenotypes (e.g., amygdala activation)?
Lets start with a

simplified example
Patients (Cases)
Allele #1
Allele #2
% Allele #1
90%
tp://vassarstats.net/odds2x2.html
Patients (Cases)
Controls
Allele #1
Allele #2
% Allele #1
90%
10%
tp://vassarstats.net/odds2x2.html
Patients (Cases)
Controls
Allele #1
Allele #2
% Allele #1
90%
10%
Allele #1 is associated
with a 9x increased risk
of disease!
(risk ratio)
sarstats.net/odds2x2.html (0.90 allele #1 = patients; 0.10 allele #2 = patient; 0.90/0.10 = 9 )
Now we need to scale this up
GWAS
- GWAS: genome-wide association study (repeat for
>1M common SNPs)
- Example: Individuals with the G-allele of SNP1
(rs1333049) were overrepresented amongst patients
(upper row) vs. controls
GWAS
- GWAS: genome-wide association study (repeat for
>1M common SNPs)
SNP1
Patients
Controls
SNP2
Etc.
How the heck are we going to

efficiently measure >1M SNPs?
Details Are Not Important
SNP Chip
SNP Chip
SNP Chip
Fragment of one strand
SNP Chip
Binds with complement
SNP Chip
Array of probes for

different gene variants
SNP Chip
Measure binding
Array of probes for
SNP Chip
Measure binding
Array of probes for
GWAS
- Brute force approachtesting one-by one the
correlation between traits and hundreds of thousands
of common genetic variants
- GWAS treats every common genomic variant the same,
allowing the discovery of novel trait- or disease
relevant genetic variants in the absence a priori
hypotheses
- The opposite of candidate gene studies that utilize
theories to test a small number of genetic variants
- Penalty is low statistical power and sensitivity, due to
correction for millions of tests across the genome
- Furthermore, GWAS will miss rare genetic variants
because they are not included on the SNP chip arrays
GWAS
hypotheses
GWAS
hypotheses
GWAS
hypotheses
(p<.05 p<.05/1,000,000)
GWAS
hypotheses
(p<.05 p<.05/1,000,000)
Why bother?
The Premise
We are pretty ignorant about the biology linking genotypes to phenotypes
(e.g., N, E, and SC). So its difficult to generate good hypotheses (candidate
genes to examine).
If we could somehow harness genetics to understand the molecular
neurobiology of T&P and associated psychiatric disorders, it would enable us
to:
-
Redefine diagnostic categories and T&P traits in terms of quantifiable etiology (root
causes)
Develop novel treatments or prevention efforts targeting links in the etiological chain
Identify at-risk individuals early (e.g., carriers of a particular polymorphism)
Precision medicine: Predict treatment response or more quickly pick the best treatment
(e.g., carriers of a particular polymorphism)
Enhance prognosis: You have 3 months to live
Monitor treatment in terms of changes in the underlying neural systems
Provide a novel discovery tool for addressing some of the most fundamental question
about the nature of T&P
- Where does extraversion come from?
The Premise
genes to examine).
to:
-
causes)
Precision medicine: Predict treatment response or more quickly pick the best treatment
(e.g., carriers of a particular polymorphism)
Enhance prognosis: You have 3 months to live
Monitor treatment in terms of changes in the underlying neural systems
The Premise
genes to examine).
to:
-
causes)
Predict treatment response or more quickly pick the best treatment (e.g., carriers of a
particular polymorphism).personalized or precision medicine
Enhance prognosis: You (and other carriers of SNP X) have 3 months to live
-
What is the biological basis of childhood shyness?
The Premise
genes to examine).
to:
-
causes)
-
The Premise
genes to examine).
to:
-
causes)
-
The Premise
genes to examine).
to:
-
causes)
-
The Premise
genes to examine).
to:
-
causes)
-
The Premise
genes to examine).
to:
-
causes)
-
Some Success with GWAS

Very recent GWASs have identified sets of
polymorphisms that collectively account for much
of the heritability of some major psychiatric
disorders
e.g., 32% variation in MDD (phenotype) can be
explained by individual polymorphisms (genes)
- Suggests that a substantial proportion of genetic
variation results from very large numbers of small
effect variants

Very recent GWASs have identified sets of genetic
disorders
- In general, recent work suggests that most genetic
effect variants

disorders
effect variants

disorders
effect variants
But theres a potential

problem
The Problem of Small Effects

- Common polymorphisms have, at most, weak effects
on brain function and behavior (e.g., 0-5%)
- Small effects are hard to detect and likely to result in
nonreplications (false negatives)
- Prompted the development of large-scale consortiums
and data-sharing networksthousands of subjects
across dozens of labs provides the statistical power
needed to reliably detect weak effects
- But this also begs the question of so what why bother
if the main effect of individual genetic polymorphisms
is so small

nonreplications (false negatives) (Study 1 hit, Study 2
null effect, Study 3 hit, etc.)
and data-sharing networksthousands of subjects
across dozens of labs provides the statistical power
needed to reliably detect weak effects
- But this also begs the question of so what why bother
if the main effect of individual genetic polymorphisms
is so small

nonreplications (false negatives) (Study 1 hit, Study 2
null effect, Study 3 hit, etc.)
and data-sharing networkstens of thousands of
subjects across dozens of labs provide the statistical
power needed to reliably detect weak effects
Whadya mean small effects?
The Case of Height
The Case of Height

Height is highly heritable (~85%) and highly polygenic,
with many variants contributing and therefore small
effect sizes for the individual polymorphisms
Using discovery and validation samples of ~130,000 and
~50,000 subjects, Lango Allen et al. discovered 180
variants
Associations were on the order of 14mm (0.02 0.2% of
phenotypic variation; ~70 mm or 7 cm)
The Case of Height

Height is highly heritable (~85%) and highly polygenic,
with many variants contributing and therefore small
effect sizes for the individual polymorphisms
Using discovery and validation samples of ~130,000 and
~50,000 subjects, Lango Allen et al. discovered 180
variants
Associations were on the order of 14mm (0.02 0.2% of
phenotypic variation)
The Case of Height

To put 4 mm (per variant) in perspective
Tony Stark (5.7 feet)

Vs.
Black Widow (5.25
feet)
= 15 cm = 150 mm
= 37.5
polymorphisms
Millimeters? What about good

old fashioned inches?
1 inch = 25.4 mm =
6.4 allelic variants
What about T&P?
contrast to height and psychopathology, GWAS studies of T&P have relied on mu

maller samples
Moor used a discovery sample of discovery samples of N = 17, 375
rvice had a discovery sample of N = 11,000
t surprisingly, they lacked the power to detect a single genetic variant that was
gnificantly associated with differences in N/NE or E/PE
ucidation of genetic loci significantly influencing temperament and personality w

equire potentially very large samples, and/or a more refined phenotype.

maller samples
Moor et al.: N = 17, 375
Service et al.: N = 11,000
gnificantly associated with differences in N/NE or E/PE


maller samples
Moor et al.: N = 17, 375
gnificantly associated with differences in N/NE or E/PE after correcting for
ultiple comparisons


maller samples
Moor et al.: N = 17, 375
gnificantly associated with differences in N/NE or E/PE after correcting for
ultiple comparisons

Are small effects a big problem?

Is the expenditure worth it?
Tiny Effects Can Be

Practically Importan
Meyer et al Amer
Tiny Effects Can Be

Meyer et al Amer
Tiny Effects Can Be

ase of Asprin
w
ecial meeting held December 18, 1987, it was decided to end prematurely a ran
blind experiment (n=22l) on the effects of aspirin on reducing heart attacks. The
unusual termination of this experiment was that it had become so clear that asp
ted heart attacks (and deaths from heart attacks) that it would be unethical to c
half the subjects a placebo. Now what do you suppose was the magnitude of the
mental effect that was so dramatic as to call for the termination of this research?
y, [it was] r = .034.
wald
as a significant (P<0.00001) reduction [from 2.16% to 1.27%] in the risk of hear
those in the aspirin group. Applying the studys estimated risk reduction of 44%
.S. Census estimate of about 46 million male U.S. residents 50 or older, regular s
of aspirin should prevent approximately 420,000 heart attacks during a 5-year pe
mer Psychol 1990; Greenwald et al JPSP in press; but see also Ferguson Rev Gen Psychol 2009
Tiny Effects Can Be

ase of Asprin
w
y, [it was] r = .034.
wald
Tiny Effects Can Be

ase of Asprin
w
y, [it was] r = .034.
wald
Tiny Effects Can Be

me Point
ects can be very practically important when they are cumulated over m
ividuals (e.g., the population of nations)
ividual experiences (e.g., many job applications, in the case of discrimin
What about more direct

evidence?
The Case of Cholesterol:

Small Effects, Big Therapeutic
Impact
Lander Nature 2011; Papassotiropoulos TiCS 2

Impact
~1 in 3 deaths
CDC 2010 Data

Impact
Cholesterol is a strong predictor of heart diseas
N = 900,000 subjects; Lancet 2007

Impact
Cholesterol is a strong predictor of heart diseas

1 mmol/L lower total cholesterol = 50%
reduction in mortality at mid-life
Cholesterol gums up your arteries
N = 900,000 subjects; Lancet 2007

Impact
Heart Disease Risk is Inherited
Cholesterol is about 50% heritable
Molecular pathways?
GWAS (N > 100,000)

Identified 95 significant SNPs
Together accounting for 10% of the phenotypic variance
and 25% of the genetic (heritable) variance
In short, each SNP only accounted for about 0.1% of the
variance in observed cholesterol levels
Sounds awful, huh?

Impact
Molecular pathways?
GWAS (N > 100,000)

Sounds awful, huh?

Impact
Molecular pathways?
GWAS (N > 100,000)

Sounds awful, huh?

Impact
Molecular pathways?
GWAS (N > 100,000)

Sounds awful, huh?

Impact
One of the 95 loci = HMGCR
HMGCR predicts modest variance in cholesterol
2.8 mg/dl
But the pathway coded by this locus is the target of the
Statins, the most popular drug for reducing cholesterol
Among the best selling drug in history ($12.4B in 05)
Clinically effective: Lower LDL cholesterol by
~1.8 mmol/l, which translates into an estimated 60%
decrease in the
number of cardiac events (heart attack, sudden cardiac
death)

Impact
One of the 95 loci = HMGCR
HMGCR predicts modest variance in cholesterol
2.8 mg/dl
But the protein coded by this locus is the target of the
Statins, the most popular drug for reducing cholesterol
Among the best selling drug in history ($12.4B in 05)
Clinically effective: Lower LDL cholesterol by
~1.8 mmol/l, which translates into an estimated 60%
decrease in the
number of cardiac events (heart attack, sudden cardiac
death)

Impact
Take Home Points
We just discovered 94 other SNPs
Lots of opportunities for understanding the molecular
mechanisms underlying one of the biggest killers
More generally small effects in a GWAS do not
necessitate small impact
Now you might be saying to yourself,

Im a fiscal conservative, what is this costing me and other taxpayers?
Are these genetic discoveries
worth it?

The Cost of GWASs: Is it Worth It??
- If we assume that the GWAS results (described in our
review) reflect a total of 500,000 SNP chips @
$500/chip = $250M
- ~2,000 variants detected in high-quality biomedical
studies (across a variety of physical and mental
disorders)
- $125,000 per discovered variant
- Good investment?
- $250M
- 1-2 stealth fighter jets
- Much less than a single navy submarine
- Fraction of the ~$9 billion cost of the LargeVisscher
et al 2012
Hadron

- Been estimated that all the high-quality GWAS studies
(circa 2012) reflect a total of 500,000 SNP chips @
$500/chip = $250M
- Detected ~2,000 genetic variants across a variety of
physical and mental disorders
- $125,000 per newly discovered variant
- Good investment?
- $250M
- Fraction of the ~$9 billion cost of the Large Hadron
Visscher et al 2012
Collider

$500/chip = $250M
- Good investment?
- $250M
Visscher et al 2012
Collider

$500/chip = $250M
- Good investment? Judgment call
- $250M
Visscher et al 2012
Collider

$500/chip = $250M
- Good investment? Judgment call
- $250M
Visscher et al 2012
Collider
Perhaps a different
strategy would be helpful?
Main Effects and Interactions

- Traditional GWAS approaches assume
that individual genes directly determine
phenotypes (T&P, disorders)
But what if traits and disorders reflect

the interaction of Genes and Experience?
What if we inherit a predisposition to be neurotic, extroverted, or conscientious,
given the appropriate environment?
G-E Interactions (G x E)
- Traits cluster in families (remember Draco Malfoy)
- But heritability appears to be probabilistic and particular

family members may not inherit a particular trait (e.g., high
levels of evilness, self-control, or depression)
- Neither genetics nor environment is solely responsible for
producing trait-like differences in phenotypes
- Individuals can inherit sensitivity to the effects of various
environmental and experiential factors
- Same pathogen, different outcomes
e.g, sunlight exposure has a much stronger influence
on skin cancer risk in the fair-skinned

environmental and experiential factors

environmental and experiential factors (diathesis)

environmental and experiential factors (diathesis)
Can apply this logic to gene

hunting
rch for combinations of genes (those contributing to skin pigmentation)

ironments (exposure to sunlight) that predict outcomes of interest
G*E Illustrative Examples

What kind of environmental factors are we talking about?
-
Family Conflict: Individuals who are genetically predisposed)to low C/SC are even more
impulsive in a conflictual family environment;
Marriage and Religiosity: Individuals who are genetically predisposed to substance

abuse are less likely to develop drinking problems if they were married or religious;
Gene*Marriage also found for MDD
Low Parental Monitoring and Substance-Abusing Peers: Individuals who are

genetically predisposed to substance use and antisocial behavior are more likely to
develop problems in these environments
In short, a wide variety of environmental factors can
(a) trigger,
(b) compensate for, or
(c) enhance genetic predisposition

-


(a) trigger,

-


(a) trigger,

-


(a) trigger,

-


(a) trigger,
(c) enhance
particular genetic predispositions
What about molecular genetics

(SNPs)?
A Famous Illustration
monoamine oxidase A
Caspi et al Science 200
Do genes interact with maltreatment to predict

antisocial behavior?
Do alleles change the slope relating maltreatment

monoamine oxidase A
Yes! Abused kids with the good allele

(gray) showed fewer antisocial behaviors
protective
monoamine oxidase A
Second Famous G*E Example
Caspi (Duke)
Caspi et al Science 2003, Amer J Psychiatry 2010; Monroe Psychol Sc
Caspi (Duke)
Caspi (Duke)
Does the impact of stress on depression

depend
on the serotonin transporter (5-HTT) gene?
Caspi (Duke)
Short
Long
Yes! Carriers of the Short allele showed a

strong positive
relationship between life stress and
depression Short allele confers risk (or the
et al Science 2003, Amer J Psychiatry 2010; Monroe Psychol Sc
Long allele confersCaspi
protection)
Key Take Home Points
Key Take Home Points for Todays

Meeting
1. T&P are somewhat heritable
2. We can use GWAS (SNP chips) to search the genome (10M
common variants) for the SNP's that account for that heritability
3. The premise of this genomic approach is nothing short of
revolutionary. We remain largely ignorant about the biological
underpinnings of T&P. GWAS provide a powerful tool for
discovering the molecular origins of T&P
Redefine T&P and associated disorders in terms of root
causes instead of self-reported symptoms
Develop novel screening procedures and interventions
grounded in an understanding of underlying mechanisms
(etiology)
4. Brute force approach. Penalty is low statistical power due to
correction for millions of tests(p<.05 vs. p<.05/1,000,000).
5. Heritable traits reflect the influence of many SNPs (polygenic),
each with a very small effect.
6. Not surprisingly, preliminary GWASs for T&P (N<20,000) have
failed to detect significant genes. Need huge samples.

Meeting
(etiology)

Meeting
(etiology)

Meeting
(etiology)

Meeting
(etiology)

Meeting
(etiology)

Meeting
7. Small effects
Are challenging and expensive to detect
Can be practically and clinically/therapeutically important
(e.g., baseball, smoking, ibuprofen)
Do not necessarily imply mechanistically worthless
(HMGCR/Statins example)
8. Yes, GWAS is expensive, but not as expensive as many other big
ticket items funded by tax payers
9. Often the impact of the environment (sunlight) on outcomes
(cancer) is dependent on genes (pigmentation). Individuals can
inherit sensitivity/diathesis.
10. In some cases, the importance of a genetic variant will only be
unmasked by examining the G-E interaction (there is no main
effect of the gene on the outcome of interest).

Meeting
7. Small effects
Can be practically important (e.g., baseball, smoking,
ibuprofen)
inherit sensitivity/diathesis.

Meeting
7. Small effects
ibuprofen)
inherit sensitivity/diathesis. G-E interaction.

Meeting
7. Small effects
ibuprofen)
inherit sensitivity/diathesis. G-E interaction.
To be continued
Genome Intermediate Phenotype
Traits (Evildoing)
Critical Thinking Take Home

Questions
Continued
1.

Questions
Pick any one of the fundamental
questions about T&P that we have
covered in class since the start of the
semester (e.g., what are the fundamental
dimensions of T&P) and then briefly
discuss how genetic information could
prove helpful for addressing that question
2.
It appears likely that genomics will play

an increasing role in medicine, and hence
is likely to have a direct impact on you
and your loved ones (directly, as
participants in a public healthcare
system, or as taxpayers funding R&D).
Identify one way in which the genomics
revolution could influence you (e.g.,
screening, precision medicine) and
discuss whether this is a positive or
negative thing. You may find it helpful to
spend a little time on Wikipedia
(https://en.wikipedia.org/wiki/Introduction
_to_genetics)
Continued
1.

Questions
dimensions of T&P). Briefly discuss how
genetic information could prove
helpful for addressing that question
2.

_to_genetics)
Continued
1.

Questions
2.

_to_genetics)
Continued
1.

Questions
2.

Identify one way in which the
genomics revolution could influence
you and discuss whether this is a
positive or negative thing. You may
find it helpful to spend a little time on
Wikipedia
_to_genetics)
Continued

Questions
3. In March 2015, researchers at Weill Cornell showed "that a single-nucleotide
polymorphism (SNP) in the fatty acid amide hydrolase (FAAH) gene of the
endocannabinoid system has parallel molecular, neural and behavioral effects in both
humans and mice engineered to express the variant human allele" (Dincheva Nature
Comm 2015)
Available @ http://www.nature.com/articles/ncomms7395.epdf?
referrer_access_token=mm5H5NOSq1Jk_TvYe8eEzdRgN0jAjWel9jnR3ZoTv0MFY2u7Zdb
RZ8yhzdTOJfaQ9HKMjv_5rGSvPOZGVRItjvxxd3D6Fuj0xbHtGY8oldf7UYS6IrqEzfzB5TJv1BbzdIXznmzLYfNCGxS84JQNwH25BbPI31H6kc8SFO8TU1kO2mN4-psU996CDETtbNnR_CIJf88376uvUOsssvlA2Iktizxf_viisyTH6B8pyD2QRPa1RJvpWrvVaNnjH&t
racking_referrer=blogs.scientificamerican.com
They note that, "Non-replication of candidate gene association studies has been a
major problem within the field of behavioral genetics. Here, we have used a parallel
mousehuman experimental approach that enables greater control for environmental
and genetic confounds. The convergent findings reported here establish that effects of
genetic variation in FAAH are evident at neural and behavioral levels in both the
mouse and in humans, providing a persuasive cross-species validation."
Continued

Questions
Comm 2015)
Continued

Questions
Comm 2015)
Continued

Questions
The report was highlighted in a provocative essay in the NY Times entitled The FeelGood Gene (6 March 2015)
Available @
http://www.nytimes.com/2015/03/08/opinion/sunday/the-feel-good-gene.html?_r=0
The author notes that
"For the first time, scientists have demonstrated that a genetic variation in the brain
makes some people inherently less anxious, and more able to forget fearful and
unpleasant experiences. This lucky genetic mutation produces higher levels of
anandamide the so-called bliss molecule and our own natural marijuana in our
brains. In short, some people are prone to be less anxious simply because they won
the genetic sweepstakes and randomly got a genetic mutation that has nothing at all
to do with strength of character."
A blogger at Scientific American
Available @
objected to both the essay and the study, noting that
"Friedmans [essay] is, in effect, an extremely dumbed down, sensationalized press

release for a highly technical article...People are desperate for genuine advances in
understanding and treating disorders such as substance abuse and pathological
anxiety. Prominent scientists such as Richard Friedman and media such as The New
York Times do these people a disservice by offering false hope based on flimsy
Continued

Questions
Available @
A blogger at Scientific American
Available @ objected to both the essay and the study, noting that
understanding and treating disorders such as substance abuse and pathological
anxiety. Prominent scientists such as Richard Friedman and media such as The New
York Times do these people a disservice by offering false hope based on flimsy
Continued

Questions
Available @
But a blogger at Scientific American
Available @ http://
blogs.scientificamerican.com/cross-check/2015/03/13/n-y-times-hype-of-feel-good-ge
ne-makes-me-feel-bad/
Continued

Questions
Available @
But a blogger at Scientific American
Available @ http://
blogs.scientificamerican.com/cross-check/2015/03/13/n-y-times-hype-of-feel-good-ge
ne-makes-me-feel-bad/
Continued

Questions
What do you think?
Take a closer look at the 3 documents. Comment on any of the following issues:
Strengths and limitations of the study

Sample size
Focus on homologous behavioral and brain phenotypes (markers) in 2
species
Procedures for manipulating and measuring anxiety
Were the authors appropriately circumspect and sober in their discussion
of the studys potential implications, or did they overreach?
Strengths and weaknesses of the NY Times essay (Over-selling? Dumbed

down?)
Strengths and weaknesses of the Scientific American rebuttal (Too quick to

dismiss? Didnt get the value of combining mechanistic models in rodents with
non-invasive measures of emotional experience and neurophysiology in
humans)
The gap between science, the media (NY Times/Scientific American), and the
public. What gets lost in translation?
Continued

Questions
What do you think?
Take a closer look at any of the 3 documents. Comment on any of the following issues:
Strengths and limitations of the study

Sample size
Focus on homologous behavioral and brain phenotypes (markers) in 2
species
Procedures for manipulating and measuring anxiety
Were the authors appropriately circumspect and sober in their discussion
of the studys potential implications, or did they overreach?
Strengths and weaknesses of the NY Times essay (Over-selling? Dumbed

down?)
Strengths and weaknesses of the Scientific American rebuttal (Too quick to

dismiss? Didnt get the value of combining mechanistic models in rodents with
non-invasive measures of emotional experience and neurophysiology in
humans)
The gap between science, the media (NY Times/Scientific American), and the
public. What gets lost in translation?
Continued
Time-Permitting
Review Questions
T&P reflect
A. Nature
B. Nurture
C. Both
Genes (nature) can influence

A. Environments
and experience
B. Neither. Nature
and nurture are
distinct and
independent
forces
Nature (heritability) is
A. Fixed and
immutable
B. Plastic and can
change in
response to
growing
autonomy or
due to
cumulative
impact
Heritability is
A. The proportion
of variation in a
trait, such as
C/SC, that is
accounted for by
the pedigree
(family tree)
B. PV/GV
C. A and B
Estimates of heritability
A. Are fixed
B. Can be influenced by
social and
environmental
influences (e.g., living
in a conservative
religious community)
that increase or
decrease the amount
of variation in the trait
(e.g., disinhibition,
partying, smoking)
Heritability
A. Is the % of
variation in a trait,
such as E/PE, that
is passed down
from your parents
B. Reflects the
inheritance of
genes, not
phenotypes or
traits
Heritability describes
A. The % of my trait that
is inherited (nature)
vs. environmental
(nurture)
B. The % of phenotypic
variation across a
group of individuals
that is influenced by
genetic factors
C. Individuals within a
population (e.g., Alex)
Highly heritable traits, such as

height
A. Are our destiny
B. Can potentially
be powerfully
influenced by
interventions
(environment)
The End
Things to Consider Adding
Somatic mosaicism: DNA differs

across neurons
Extra Slides
A few interim take home points

1. Recap: What % of the variance in T&P (phenotype) is due to
genes/nature vs. environment/nurture?
2. What is heritability (h2)? What are the limitation of this
parameter? What are common misconceptions about h2?
3. What has psychiatric genetics taught us?
4. What are the long-term prospects for linking heritable traits
(e.g., T&P) to distinct neurobiological systems?
5. There is a considerable excitement about so-called neurogenetic
approaches that combine measures of molecular genetic
variation (SNPs) with measures of brain function (fMRI). What
are the seminal observations? What are some of the key
challenges facing the nascent field of neurogenetics?
6. What are G*E interactions? How does genetic influence depends
on the environment?
7. How does the environment get under the skin?
What about the brain?
Genome Intermediate Phenotype
Traits (Evildoing)
Bogdan (Wash U)
The Neurogenetic Strategy

Link genetic variation (polymorphisms) to variation in brain structure and
function (MRI)
Address how genes influence behavior remember, heritability does not
address biological mechanism!
- by correlating genetic variation with intermediate biological phenotypes (e.g.,
amygdala
activation), we can discover testable mechanisms for genetic influence
on behavior
Address the molecular mechanisms linking genes to brain to behavior

- its hard to directly measure neurochemistry (e.g., serotonin levels in the
amygdala) in humans
- If we measure a genetic polymorphism with a known function (e.g., serotonin
transporter SNP)
- and we are willing to make some assumptions (differences in the SNP have
predictable effects
on gene expression and ultimately serotonin levels in the
amygdala)
- then we can use genetic variation (polymorphisms), which we can noninvasively
measure in humans, as a proxy for individual differences in neurochemistry

function (MRI)
amygdala
on behavior
- can address questions such as, Why is the amygdala hyper-reactive in
behaviorally inhibited individuals?
Potentially address the molecular mechanisms linking genes to brain to

behavior
amygdala) in humans
transporter)
- and we are willing to make some assumptions (differences in the poly. have
predictable effects

function (MRI)
amygdala
on behavior

behavior
amygdala) in humans
transporter)
predictable effects

function (MRI)
amygdala
on behavior

behavior
amygdala) in humans
transporter)
predictable effects

function (MRI)
amygdala
on behavior

behavior
amygdala) in humans
transporter)
predictable effects
Seminal Example: Amygdala & 5HTTLPR
- Threat-related amygdala reactivity is correlated with

variation in the serotonin-transporter linked
polymorphic region (5-HTTLPR) on the SLC6A4 gene
- S allele is bad: Individuals with the less

transcriptionally-efficient short allele (fewer transporter
proteins available to clear serotonin from the synapse)
show heightened threat-related amygdala reactivity
relative to individuals with the long allele
- Gene Amygdala: Meta-analyses suggest that the
5-HTTLPR genotype accounts for 2-5 of the variance in
amygdala reactivity
- Gene Amygdala MDD: Evidence that these
genetically conferred differences in amygdala
reactivity mediate some of the association between


relative to individuals with the long allele
- Gene Amygdala: Meta-analyses suggest that the
5-HTTLPR genotype accounts for 2-5 of the variance in
amygdala reactivity


relative to individuals with the long L allele
- Gene Amygdala: Meta-analyses suggest that 5HTTLPR accounts for 2-5% of the variance in amygdala
reactivity


relative to individuals with the long L allele
- Gene Amygdala: Meta-analyses suggest that 5HTTLPR accounts for 2-5% of the variance in amygdala
reactivity
reactivity mediate some of the association between 5-
The Problem of Assumptions

These data suggest the following etiologic chain:
[GENETIC OBSERVATION] 5-HTTLPR
[ASSUMPTION] reduced efficacy of 5HTT (protein)
[ASSUMPTION] too much 5HT in amygdala synapses
(chemistry)
[NEURAL OBSERVATION] increased amygdala
reactivity to threat
[EPIDEML OBSERVATION] MDD, especially among
individuals exposed to stress
he Problem of Assumptions
Kalin (UW)
No relation between polymorphism and amygdalar

5HTT expression
when you actually go in and measure the
transporter using PET
our findings are in agreement with the majority of
human PET studiesthat suggest there is not a
detectable relationship between in vivo 5-HTT binding
and s-allele carrier status our work in the rhesus
monkey, and that of others in humans, calls into question
Alex stop here / do epigenetics

next time
Brief Aside on How the Environment

Gets Under the Skin
Students:
whats a plausible mechanism?
How might parenting or exposure to other risks influence behavior (phenotype)?
How Does E Get Under the Skin?

Epigenetics provides a biological explanation for how E (parenting, therapy, life
events) alters behavior
-
The environment (e.g., learning, stress) can alter gene expression (protein synthesis)
without altering the genome (DNA; hence, not heritable)
Gene expression is influenced by transcription factors, which bind to sequences of DNA
Binding of transcription factors turns genes on or off
Epigenetic mechanisms involve changes to how readily transcription factor can access
the DNA
E.g., methylation: addition of a methyl group onto a cytosine (1 of the 4 base
pairs that make up DNA) silences the gene because methyl hinders the
transcription factors
-
Epigenetic modifications of the genome have long been known to exist e.g., all cells in
the body share the same DNA; accordingly, there must be a mechanism whereby
different genes are active in liver cells vs. neurons
Work in rodents by Michael Meaneys group demonstrates that maternal behavior can
influence the adult T&P of offspring and that this is epigenetic dependent

-
the DNA
-
Work in rodents by Michael Meaneys group demonstrates that maternal behavior (xfostered) can influence the adult T&P of offspring and that this is epigenetic dependent

-
the DNA
-
Elegant mechanistic work in rodents by Michael Meaneys group demonstrates that one
aspect of the early environment , maternal behavior (x-fostered), can influence the T&P
of offspring and that this is epigenetic dependent
This is exceedingly hard to study in humans because epigenetic mechanisms vary across
the brain and body, so measuring epigenetic effects in blood or saliva may not tell you
PSYC 612 R08B:

G-E Correlations:
How Genes Get Outside the Skin
AJ Shackman
9 December 2013
PSYC 612 R08B:

G-E Correlations:
How Genes Get Outside the Skin
Students?
Lemery (ASU)
Jaffee (Penn)
G-E Correlations Defined (Plomin

77)
Many sources of influence that we might consider environmental are actually
non-random and genetic
1. Passive G-E correlation (nature and nurture are confounded)
- among biologically related parents and offspring, the parents provide genotypes
AND rearing environment; thus many parent-child outcome correlations may
actually reflect passive G-E effects
-
E.g., the reason children who are spanked or smacked are more aggressive than
children who are not may be that parents and kids share a genetic risk for
aggressive behavior (common cause)
2. Evocative G-E correlation

- e.g., a child who is predisposed to having an outgoing, cheerful T&P is more likely to
evoke positive attention from others than a child who is predisposed to N/NE
E.g., Individuals with a grumpy, abrasive temperament (N/NE) tend to evoke
unpleasant responses
from coworkers and others than cheerful, friendly individuals
-
3. Active G-E correlation

- Individuals actively select environments
- E.g., individuals predisposed to high E/PE seeking may be more prone to attend
parties, go to bars, meet new people, be exposed to or to try substances of abuse

77)

AND rearing environment; thus many parent-child outcome correlations reflect
passive G-E effects
-

E.g., Individuals with a grumpy, abrasive temperament (N/NE) tend to evoke
unpleasant responses
from coworkers and others than cheerful, friendly individuals
-


77)

passive G-E effects
-

-
E.g., Infant behavioral inhibition evokes parental insensitivity, which then

potentiates
maladaptive parentchild interactions over time, exacerbating fear of novelty


77)

passive G-E effects
-

-
E.g., Infant behavioral inhibition evokes parental insensitivity, which then

potentiates
maladaptive parentchild interactions over time, exacerbating fear of novelty
3. Active G-E correlation (Niche Building)

-
E.g., individuals predisposed to high E/PE seeking may be more prone to attend
parties, go to bars, meet new people, be exposed to delinquent peers, and try
Evidence for G-E Correlations

Mostly from FTA studies demonstrating that environmental measures are
heritable, including many linked to psychopathology
e.g., marital quality, social support, parental discipline/warmth, family environment,
peer relationships, negative life events such as divorce and exposure to trauma
Environments are heritable because genotype influences behaviors that evoke,
select, and modify features of the environment
- Environments less amenable to behavioral modification are less heritable, e.g., the
death of a loved one, losing ones home in a natural disaster
- Than those that depend on the individuals behavior, e.g., divorce, getting fired
Take home: Genetic risk factors do not necessarily have direct effects on phenotypes (T&P,
Dx), but can work indirectly by modifying sensitivity to environmental risk factors (active GE) or by influencing exposure
to risk (passive, evocative G-E)

Mostly from FTA studies demonstrating that environmental measures are
heritable, including many linked to psychopathology
e.g., marital quality, social support, parental discipline/warmth, family environment,
peer relationships, negative life events such as divorce and exposure to trauma
Environments are heritable because genotype influences behaviors that evoke,
select, and modify features of the environment
- Environments less amenable to behavioral modification are less heritable, e.g., the
death of a loved one, losing ones home in a natural disaster
- Than those that depend on the individuals behavior, e.g., divorce, getting fired
Take home: Genetic risk factors do not necessarily have direct effects on phenotypes (T&P,
Dx), but can work indirectly by modifying sensitivity to environmental risk factors (active GE) or by influencing exposure
to risk (passive, evocative G-E)
G-E Correlation Take Homes

3 Kinds of G-E Correlations: Passive, Evocative,
and Active
Take home: Genetic risk factors do not necessarily have
direct effects on phenotypes (T&P, Dx), but can work
indirectly by modifying exposure to environmental risks
(e.g., stress, substances, delinquent peers) that reinforce
particular personality traits or precipitate frank
psychopathology
More fundamentally, these data emphasize that
Nature/Genotype and Nurture/Environment are not
mutually exclusive forces, but often work together to
increase or decrease the likelihood of important
outcomes
Long Term Prospects, The Good

We could get lucky
In the most optimistic scenario, nearly all of the verified risk genes identified
through GWAS or sequencing will map to a single coherent inter-connected
biological pathway.
This will occur only if the genetic underpinnings of the disorder reflect a high
degree of etiological homogeneity. i.e. a single disease process
(equifinality)
Intermediate scenarios (neither Ugly nor Good) are possible
Long Term Prospects, The Ugly

There are many many ways to make a neuron hypofunction
(shrunken
dendrites, too few or dysfunctional receptors, downregulated 2 nd
messenger systems, or deficient transport mechanisms.
There are even more pathways to make a complex
circuit dysfunction
This scenario is likely if there are hundreds of distinct biochemical
changes that individually contribute to Dx (neither necessary nor
sufficient) with independent pathways to the phenotype.
Perhaps there are too many ways for the human brain to produce
symptoms/signs of psychiatric disorders (for example, sad mood, auditory
hallucinations, grandiosity) for a limited number of biologically coherent
pathways to emerge from the 100s or 1000s of genes that make small
contributions to risk.
Here, psychiatric disorders (or T&P) arise at such a high level within the
mindbrain system that we have no way to integrate GWAS or sequencing
findings.
Neurogenetics Take Homes

1. There is considerable excitement about the neurogenetics approach.
2. This reflects both clinical interests (Tx) as well as the basic science hope that it can
provide clues about the molecular differences that influence the effects seen in fMRI
studies (e.g., understand influence of 5HT without actually measuring 5HT).
3. But assumptions may not be warranted; e.g., 5HTTLPR is unrelated to transporter
expression in amygdala
4. Neurogeneticists face all of the problems outlined by Kendler: The Broken Glass, and,
The Jet Mechanic. No guarantee that there are a limited number of functionally coherent
substrates to be identified.
5. The effects of single polymorphisms, such as 5HTTLPR, tend to be weak, necessitating
large, expensive samples and begging questions about cost/benefit.
6. G*E approaches (life stress and 5HTTLPR) have led to much excitement, and may
unmask bigger effects and increased understanding. But at times, it feels like a fishing
expedition.
7. Likewise, G*G interactions (epistasis) and multilocus profiles that address the aggregate
effect of many small-effect genes may prove helpful, but seem to lead back to the black
box of aggregate h2 measures.
8. Combinatorial complexity is daunting (6M variants!). More sophisticated modeling and
machine learning approaches will be needed. The primate brain is too stupid to decipher
the human brain without help.
Translational Promise
Sara argues that, in principle, if one could identify with high sensitivity and
specificity at-risk G-E pairs
- At-risk kids paired with risky environments (parental style, peers, adversity, abuse,
etc.)
You could target them for precision interventions BEFORE the onset of cumulative
damage
- in effect, she argues for a more nuanced extension of the Moffitt PNAS strategy
- instead of identifying kids with low C/SC
- identify kids with low C/SC and other environmental risk factors
- this is akin, as I understand it, to what Andreas lab does (ADHD kid + parent with
sub-optimal skill)
- potentially, one could use biomarkers (gene screens) to identify high-risk parent-kid
dyads
More Sophisticated Approaches:

Gene*Gene & Multilocus Profiles
The phenotype (T&P/Dx) reflects the cumulative effect of all
the genes; traits are massively polygenic
In principle, it would be helpful to model gene*gene
interactions or develop more complex additive (many main
effects) profiles (high on this, medium on that, low on the
other and so on)
In practice, this is challenging given the combinatorial
complexity
Also, profile scores that combine many genes eliminates the
possibility of testing specific mechanistic hypotheses in animal
models, back to black box of aggregate heritability
There is considerable excitement about the development of
more sophisticated analytic tools (e.g., machine learning of
More Sophisticated Approaches:

Gene*Gene & Multilocus Profiles
The phenotype (T&P/Dx) reflects the cumulative effect of all
the genes; traits are massively polygenic
In principle, it would be helpful to model gene*gene
interactions or develop more complex additive (many main
effects) profiles (high on this, medium on that, low on the
other and so on)
In practice, this is challenging given the combinatorial
complexity
Also, profile scores that combine many genes eliminates the
possibility of testing specific mechanistic hypotheses in animal
models, back to black box of aggregate heritability
There is considerable excitement about the development of
more sophisticated analytic tools (e.g., machine learning of
Bogdan (Wash U)
The G*E Strategy

- Ryan and Ahmad argues that examining G*E
interactions is more realistic
- insofar as we believe (e.g., the material covered in
prior lectures) that psychopathology and T&P reflect
the interaction of genetically endowed diatheses
and negative life events (e.g., stress, adversity,
abuse, loss) and learning
- and not the direct consequence or main effect of
either G or E
- Ryan argues that the effects are likely to be
bigger as well
Some Take Homes

1. There is considerable excitement about the neurogenetics approach.
2. This reflects both clinical interests (Tx) as well as the basic science hope that it can
provide clues about the molecular differences that influence the effects seen in fMRI
studies (e.g., understand influence of 5HT without actually measuring 5HT).
3. But assumptions may not be warranted; e.g., 5HTTLPR is unrelated to transporter
expression in amygdala
4. Neurogeneticists face all of the problems outlined by Kendler: The Broken Glass, and,
The Jet Mechanic. No guarantee that there are a limited number of functionally coherent
substrates to be identified.
5. The effects of single polymorphisms, such as 5HTTLPR, tend to be weak, necessitating
large, expensive samples and begging questions about cost/benefit.
6. G*E approaches (life stress and 5HTTLPR) have led to much excitement, and may
unmask bigger effects and increased understanding. But at times, it feels like a fishing
expedition.
7. Likewise, G*G interactions (epistasis) and multilocus profiles that address the aggregate
effect of many small-effect genes may prove helpful, but seem to lead back to the black
box of aggregate h2 measures.
8. Combinatorial complexity is daunting (6M variants!). More sophisticated modeling and
machine learning approaches will be needed. The primate brain is too stupid to decipher
the human brain without help.
Strategy for Linking FTA to

Molecules
Dick notes that it is useful to first search for G*E interactions in FTA studies
There are a huge number of environmental factors that could potentially be assessed
Useful to build off the already well-developed developmental literature
In cases where there is an interaction between Genes (in aggregate) and Environment (e.g.,
peer delinquency exposure), that is, a hit in the FTA literature
It makes sense to drill down into specific genes, either candidate variants or GWAS
R08A/B Key Learning Objectives

1. Recap: What % of the variance in T&P (phenotype) is due to
genes/nature vs. environment/nurture?
2. What is heritability (h2)? What are the limitation of this
parameter? What are common misconceptions about h2?
3. What has psychiatric genetics taught us?
4. What are the long-term prospects for linking heritable traits
(e.g., T&P) to distinct neurobiological systems?
5. There is a considerable excitement about so-called neurogenetic
approaches that combine measures of molecular genetic
variation (SNPs) with measures of brain function (fMRI). What
are the seminal observations? What are some of the key
challenges facing the nascent field of neurogenetics?
6. What are G*E interactions? How does genetic influence depends
on the environment?
7. How does the environment get under the skin?
Goldsmith Slides
2. Two major types of genomic variants

1. Sequence variants
-SNPs
-single insertions & deletions
2. Structural variants (major categories)

-tandem repeats (also called microsatellites)
-triplet repeats (also called minisatellites)
-CNVs (copy number variants), to be
discussed soon
The genome
3.1-3.2
billion bases
~21-23,000
genes
The most common type of genetic

variantthe SNP
SNP = single nucleotide
polymorphism
usually diallelic (2/3rd are C/T)
SNPs account for 90% of human genetic
variation
In the human genome there are an estimated
10,000,000 - 11,000,000 common SNPs (with
> 1% frequency) (dbSNP)
Occur once in 300 bases
~7,000,000 SNPs have been identified and
provisionally mapped
Microsatellite Markers: e.g., Tandem Repeats

CACACACACACACACACACACACAGAGTGAGCTAACTCACATTAATTGCGTTGC
ATTGTTATCCGCTCACAATTCCACACAAT
6 repeat units
CACACACACACACACACACACACACACACACACACAGAGTGAGCTAACTCACATTAATTGCGTTGC
ATTGTTATCCGCTCACAATTCCACACAAT
9 repeat units
frequently found within the genome
highly polymorphic
Minisatellite Markers: 10-100 bp repeats (e.g., in Fragile X)
ariation in the number of copies is likely due to neighboring

s-acting meiotic double-strand break hotspots
Copy Number Variants (CNVs)

A structural variant in the DNA rather than a
sequence variant (such as a SNP)
Regions of genomic DNA (>1000 bases in
length, up to 5 megabases) that can be
duplicated or deleted
The Human Genome Project showed copy
number variation to be common. A comparison
of 2 individuals showed 297 possible CNV
differences across the genome.
CNVs can occur within one gene or involve >1
gene. Thus, CNVs involving dosage-sensitive
genes can have functional significance.
CNVs may be especially important in speciation
(human vs. chimp differences in CNVs are
prominent)
3. Three stages of human behaviorgenetic investigation

1. Quantitative genetic approaches to estimate
overall genetic variance
-Family (pedigree), twin, & adoption designs
2. Gene discovery approaches (this week)
3. Gene environment interplay, and other
functional investigations with identified genes
(last unit of course)
-Overlap and integration of approaches; e.g., twin
designs used in all 3 approaches, esp. #1 & #3
4. The two major classifications of disorders

that determine which methods of gene
identification should be pursued
21 rare alleles
3 common alleles
Models of Common Inherited

Disease
Common DiseaseCommon Variant
(CDCV)
Risk alleles are

common, > 5%
Selection is weak
Risk mutations are old
Limited # of alleles
oligogenic
Risk alleles have weak
to moderate effects on
phenotypes
Risk alleles are shared
across populations
Common DiseaseRare Variant (CDRV)

Risk alleles are rare, <
1%
Selection is strong
Risk mutations are
recent
Large # of alleles
genetic heterogeneity
Range of strengths of
effects
Risk alleles are
Out of Africa
5. The three major methods of gene

discovery/identification
A. Linkage
B. Allelic Association
-Direct
-Indirect
Next, linkage
Gene
Identification
Where to look
Targeted
Linkage or Cytogenetic Positional
candidate
Pathophysiology Candidate gene
Animal models
Genome-wide
How to look
A. Linkage analysis
B. Association Studies
Genetic linkage two loci that reside

physically near each other on the same
chromosome. Linkage can result in a
within-family association between a
genetic marker and disease status
Genetic marker polymorphic DNA
sequence (typically not functional) of
known chromosomal location
Recombination -- rate at which
disease status is assoc. with different
genetic marker status in offspring than
parents (range is 0% to 50%)
A. Linkage our
experience with linkage so
far in this course
An intuitive example of
linkage analysis for a
polygenic trait
- The affected sib pair
method, (analyzing
allele sharing)
Sample, disorder, set of markers
Linkage Analysis:
formal definition
Statistical procedure for analyzing
within-family associations between
genetic markers and disease
phenotypes that takes into account
the complications of reduced
penetrance and crossing-over.
Test statistic = lod score
Lod Score (the measure

of linkage)
lod = log10 (odds[linkage:no
linkage])
odds = probability linked at (
<.50)
probability unlinked (
=.50)
(theta is the recombination frequency between
the marker and unknown disease gene; theta
can be tested at values between 0 and .50)
lod is considered significant if >
Lod Scores
Lod Score
Odds for Linkage
-3
1:1000
-2
1:100
-1
1:10
10:1
100:1
1000:1
An early linkage study:

Sherrington et al.
(1988)
Targeted 5q11-5q13 in 7 pedigrees
(104 individuals with 44 affected)
Assumed schizophrenia was
autosomal dominant with 86%
penetrance.
Lod score = 6.5 at = .08
(odds better than 3,000,000:1).
Genome-Wide Linkage
Analysis
Targeted Linkage Approach
Depends on fortuitous
observations
Genome-Wide linkage
Approach
Need a marker AT LEAST every ~
10cM 300-400 markers
Summary on Linkage Analysis

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
Does not find the gene, rather identifies a
B. Allelic Association
Association between allele status
and phenotype in unrelated
individuals. Population-level
association
OR = 60*60 = 2.25
40*40
Not O
(A,B,AB)
O
Stomach Cancer
60
40
40
60
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.
Genetic Association Strategies

Non-targeted:
genome-wide
Targeted:
Chromosomal anomaly (e.g., VCFS)
Biologically based hypotheses (e.g.,
DRD4 and Novelty-seeking)
Animal models
Positive linkage results
Expression studies
The Age of Discovery: A Gene For

...
Date
New York Times Headline
2-26-1986
Defective gene tied to form of manic-depressive illness
11-10-1988
Schizophrenia study finds strong signs of hereditary cause
4-18-1990
Scientists see linkage between alcoholism and a single

gene
7-16-1993
Report suggests that homosexuality is linked to genes
10-22-1993
Gene tie to male violence is studied
1-02-1996
Variant gene tied to love of new thrills
And the Age of Loss ...

Date
New York Times Headline
2-26-1986
1-13-1993
Defective gene tied to form of manic-depressive illness

Scientists now say they cant find gene for manic-depressive illness
11-10-1988
11-07-1989
Schizophrenia study finds strong signs of hereditary cause

Scientists now doubt they found faulty gene linked to mental illness
4-18-1990
Scientists see linkage between alcoholism and a single gene
7-16-1993
4-23-1999
Report suggests that homosexuality is linked to genes

Study questions gene influence on homosexuality
10-22-1993
2-14-1992
Gene tie to male violence is studied

Genes dont doom anyone to a life of crime
1-02-1996
11-01-1996
Variant gene tied to love of new thrills

Maybe its not a gene behind a persons thrill-seeking ways
Allelic Association
Advantages
Easy design to implement
Compares cases versus controls
In principle, very high statistical power
In principle, can identify causal agent
Disadvantages
Need to know functional polymorphisms
in a candidate gene (for direct
association)
Concern about false-positives due to
mis-matching cases and controls
(stratification bias next slide)
hnic Group #1: OR = 1.0

Hyper
+
Hyper
24
(.40)
16
(.40)
40
(.40
)
Not
O
36
24
60
60
40
100
Group #2: OR = 1.0

hnic Group #1: OR = Ethnic
1.0
Hyper
+
Hyper
24
(.40)
16
(.40)
40
(.40
)
Not
O
36
24
60
60
40
100
Hyper
+
Hyper
9
(.10)
1
(.10)
10
(.1
0)
No
t
O
81
90
90
10
100
hnic Group #1: OR = 1.0

Ethnic Group #2: OR = 1.0
Hyper
+
Hyper
24
(.40)
16
(.40)
40
(.40
)
Not
O
36
24
60
60
40
100
Combined:
OR = 1.83
Hyper
+
Hyper
9
(.10)
1
(.10)
10
(.1
0)
Not
O
81
90
90
10
100
Hyper
+
Hyper
33
(.22)
17
(.34)
50
(.25
)
Not
O
117
33
150
Why the False-Positive Findings?

Stratification bias (ethnic
mismatching)
Winners Curse
Initial significant findings overestimate
the magnitude of the effect
Cumulative Odds Ratio as a Function of

Publication Year
Original
OR=8.7
ith et al. (2008) American Journal of Epidemiology, 167(2): 125-1
Cumulative Odds Ratio as a

Function of Publication Year
Pooled 1st &
2nd OR= 3.9
Original
OR=8.7
Cumulative Odds Ratio as a

Function of Publication Year
Original
OR=8.7
Winners Curse
Cumulative Odds Ratio as a Function of
Publication Year
Original
OR=8.7
Final OR=1.4
Why the False-Positive

Findings?
Ethnic mismatching
Winners Curse

Genetic effects smaller than previously
thought
Gene-environment Interaction
G effect may only exist in certain
environments
(reminder: heritability estimates are
Why the False-Positive

Findings?
Ethnic mismatching
Winners Curse

Genetic effects smaller than previously
thought
Gene-environment Interaction
Effect may only exist in certain
environments
APOE
Polymorphism
Allele-specific Odds Ratios (ORs) for

Polymorphisms Significantly
Associated in Meta-Analyses of Alzheimers
Disease
Recap: Finding genetic effects has

been difficult
Expected effect sizes
overestimated
Winners curse non-replication
Sample sizes were too small
Meta-analyses likely give more accurate
estimates
Assumption that genetic variants

are common may not always be
accurate
Returning to the big picture of

gene identification
Non-targeted, genome-wide
approaches
Possible with linkage
Until recently, not possible with
association
Early-stage strategy: generates
candidates
Targeted approaches (e.g.,

candidate gene)
Require specific hypotheses
(sometimes driven by feasibility more
Returning to the 3 approaches

Linkage analysis: within family
association between marker and
phenotype
Genetic effects may not be strong
enough
Allelic (Direct) Association:
population association between
presumed causal variant and phenotype
May not know enough for specific
hypotheses
Thus, we often must rely on
Linkage Disequilibrium, or Indirect
Association:
Indirect and Direct Allelic

Association
Direct Association
D
Assess relationship of D locus
to phenotype directly
expect D to be a functional
polymorphism in a candidate gene
Indirect Association
M1 M D M3
2
Assess relationship of D locus

indirectly by determining whether
markers (Mi) are associated with
disease Mi dont need to be
functional
Haplotypes
Haplotype is a generalization of the
concept of a single genotype to
multiple linked loci refers to a
series of markers (usually SNPs)
Haplotypes
Haplotype is a generalization of the
concept of genotype to multiple loci
Recombination is not random, but rather
tends to occur at hot spots
This gives rise to blocks of DNA
(haplotypes), where there is very little
recombination within blocks but extensive
recombination between blocks
STOPPED HERE
Haplotypes
A
3 Genotypes:
AT at locus 1
CG at locus 2
GC at locus 3
Haplotypes
(alleles inherited
together on a
segment of the
same
chromosome)
ACG & TGC
Haplotype Blocks
rdon & Abecasis (2003). Using haplotype blocks to map the human geno
ends in Genetics, 19: 135-140.
Although 9 markers in block 4,

only 4 possible haplotypes, which
can be determined by only 3 marke
rdon & Abecasis (2003). Using haplotype blocks to map the human geno
ends in Genetics, 19: 135-140.
Linkage Disequilibrium Mapping

Because of linkage disequilibrium,
inheriting a marker allele might be
a (imperfect) indication of having
inherited a chromosomal segment
with a certain mutation. This will
depend on
The number of generations since
introduction of the original mutational
event
How tightly linked the marker allele
and the certain mutation are
Out of Africa
Empirical Evidence
CDCV model & LD

If variant is common and not
selectively advantageous, it must
be ancient.
That is, the mutation probably
existed when all humans were in
Africa (maybe 2500-4000
generations ago).
LD may only extend up to 3 kb
would need about 500,000
markers at this spacing to cover
Illumina 1M DNA Analysis BeadChip
Lessons From Height
Twin studies high heritability (~ 80-90%)

Genes (mendelian) causing extreme stature are known
Genes (polygenic) causing normal height variation were not known
Lessons From Height

Despite high heritability estimates the
results have been disappointing and
inconsistent, with reports of quantitative trait
loci (QTLs) scattered across the genome and
rarely replicated.
Perola, M. et al. (2007). PLOS Genetics, 3(6):
1019.
Note the dates of papers/quotes
Lessons From Height

In the past 18 months, the first robust common
variant associations were identified and there
are now 44 loci known to influence normal
variation in height.
Weedon, M.W. & Frayling, T.M. (2008). Trends
in Genetics, 24: 595-603.
Replicated GWAS for Height

(Total N > 160,000)
Replicatio
Significan
n
t Findings
N
29,098
1 variant
Study
Original
N
Weedon (2007)
4,921
Sanna (2008)
6,669
28,801
1 variant
Weedon (2008)
13,655
16,482
Gudbjartsson
(2008)
Lettre (2008)
29,820
8,541
15,821
> 10,000
20
variants
27
variants
12
variants
Average Effect of Replicated

Genetic Variant = ~0.3-0.4 cm
% Height Variance Accounted For
Goldstein, D.B. (2009). Common genetic variation and human

traits. NEJM, 360: 1696-1698
the latest on GWAS of

Height
Yang et al. (2010) take a classical quantitative genetic
approach to this problem by using genome-wide genotypes to
infer the genetic relatedness of individuals and then estimate
the relationship of this quantity to phenotypic similarity, thus
arriving at an estimate of heritability explained.
Their model complex trait is height, which has heritability of
~80%, only approximately 5% of which has been explained
by 50 common polymorphisms identified by GWAS.
Starting with a Brisbane, Australia cohort of 3,925 unrelated
individuals (who have less genetic relatedness than typical
second cousins), they in effect linearly regress all of the SNPs
from their GWAS onto an appropriately adjusted measure of
height.
The raw estimate that this produces is that 45% of the total
variation for height (and hence 56% of the heritability) in the
Brisbane cohort can be explained by common SNPs (regardless
of their significance).
By accounting for imperfect linkage disequilibrium between
tagging and causal variants, Yang et al. up their estimate of
common variant effects from 56% to at least 67% of the genetic
contribution to height.
A further correction assumes that causal variants are likely to be
deleterious and hence at lower frequency than tagging SNPs,
and in this case leads to the conclusion that most of the
heritability for height can be captured by common variants.
This presents an elegant argument that most of the

heritability is hidden rather than missing and, hence, that
there is no pressing need to invoke more complex genetic
mechanisms to explain height. Whether or not this is also
true of susceptibility to common diseases remains to be
determined.
Furthermore, there is the caveat that this interpretation of the
result is a parsimonious one and that a variety of genetic
models could also produce similar regressions of phenotypic
on genetic relatedness.
Most commentary from Gibson, 2010, Nature Genetics
MAF & Odds Ratios of GWAS

Associations
Median =
1.33
Hindorff, L. A. et al. (2009). Potential etiologic and functional

implications of genome-wide association loci for human
diseases and traits. Proceedings of the National Academy of
GWAS appears successful as

newer, larger studies are
reported
18 loci in sample of 249,79

account for 1.5% of varianc
in BMI

account for ~10% of varianc
in height

account for 3.6-6.1% of varia
in age at menarche
GWAS of Behavioral
Traits
As of Jan., 4, 2010 at:
Design:
~3300 Sz and 3600
Controls
1M SNP markers
Results:
Most highly associated
SNP
had p = 3.4 x 10-7
Second most highly
http://www.genome.gov/GWAStudies/index.cfm?pageid=26525384#searchForm
Maher, B. (2008). Personal genomes: The case of the missing

heritability. Nature, 456(7218), 18-21.
The 5 most probable reasons that GWAS have

failed to account for the missing heritability
Studies are not powerful enough, re
sample sizes and number of markers;
found genes that are not significant
are important
G x G interactions (epistasis) and G x
E interactions prevalent, but studies
are not powered to find these
interactions
Genetic heterogeneity is common
phenotype definition is poor (esp for
behavioral phenotypes)
Many of the important variants are not
If heterogeneity is
common,
Then, rare variants (which would
be population specific) might
explain part of the heritability not
explained by common variants.
Models of Common Inherited

Disease
Common DiseaseCommon Variant
(CDCV)
Risk alleles are common

> 5%
Selection is weak
Risk mutations are old
Limited # - oligogenic
Weak to moderate
effects
Shared across
populations
Common DiseaseRare Variant (CDRV)

Risk alleles are rare
< 1%
Selection is strong
Risk mutations are
recent
Large # heterogeneity
Range of effects
Population specific
Recurrent CNVs
McCarthy, S. E., Makarov, V., Kirov, G., Addington, A. M., McClellan,

J., Yoon, S., et al. (2009). Microduplications of 16p11.2 are
associated with schizophrenia. Nature Genetics, 41(11), 1223-1227.
Conclusions: Gene
Identification
Common Disease, Common Variant:
Can now do genome-wide studies
Effect of any variant will be very small
Require large samples, consortia & metaanalysis
Clinical implications uncertain
Common Disease, Rare Variant:

Cannot do genome-wide association studies
Rare variants could have large effects
Require large, evolutionarily homogenous
populations (e.g., Finland)
Could have significant clinical implications
Type of
Association
Interpretation
Genome-wide
Resolution
Preferred Sample
Sensitivity
Specificity
Linkage
Allelic
Association
(Direct)
w/i Family
between
marker and
phenotype
Pop assoc btw

functl poly and
phenotype
Linkage
Disequilibrium
(Indirect)
Pop assoc btw
marker and
phenotype
Allelic
Association
(Direct)
Linkage
Disequilibrium
(Indirect)
Within family
between
marker and
phenotype
Pop assoc btw functl

poly and phenotype
Pop assoc btw

marker and
phenotype
Region
implicated
Gene or nearby
gene
implicated
Region
implicated
Linkage
Type of Association
Interpretation
Genome-wide
Resolution
Preferred Sample
Sensitivity
Specificity
Linkage
Disequilibrium
(Indirect)
Linkage
Allelic Association
(Direct)
Type of Association
w/i Family between

marker and
phenotype

poly and phenotype
Pop assoc btw

marker and
phenotype
Interpretation
Region implicated
Gene or nearby gene

implicated
Region implicated
No, maybe in
the future
(~60,000)
Now feasible
(~500,000,
HapMap)
Genome-wide
approach?
Resolution
Preferred Sample
Sensitivity
Specificity
Yes, 300-400
markers
Linkage
Disequilibrium
(Indirect)
Linkage
Allelic Association
(Direct)
Type of Association
w/i Family between

marker and
phenotype

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
(~60,000)
Now feasible
(~500,000, HapMap)
Resolution
Preferred Sample
Sensitivity
Specificity
Typically w/i 810

centimorgans
recombination
Not relevant
Typically
<< 1
centimorgan
Linkage
Disequilibrium
(Indirect)
Linkage
Allelic Association
(Direct)
Type of Association
w/i Family between

marker and
phenotype

poly and phenotype
Pop assoc btw

marker and
phenotype
Interpretation
Region implicated
Gene or nearby gene

implicated
Region implicated
Genome-wide
Not now but maybe

in the future
(~60,000)
Now feasible
(~500,000, HapMap)
Resolution
Typically w/i 8-10

centimorgans
recombination
Not relevant
Typically (much) less

than 1 centimorgan
Unrelated
individuals
Genetic isolates
if rare
Preferred
Sample
Sensitivity
Specificity
Large pedigrees
Sib pairs
Linkage
Disequilibrium
(Indirect)
Linkage
Allelic Association
(Direct)
Type of Association
w/i Family between

marker and
phenotype

poly and phenotype
Pop assoc btw

marker and
phenotype
Interpretation
Region implicated
Gene or nearby gene

implicated
Region implicated
Genome-wide
Not now but maybe

in the future
(~60,000)
Now feasible
(~500,000, HapMap)
Resolution
Typically w/i 8-10

centimorgans
recombination
Not relevant

than 1 centimorgan
Preferred Sample
Large pedigrees
Sib pairs
Unrelated
individuals
Genetic isolates
if rare
Sensitivity
Relatively low
Relatively High
Relatively High
Specificity
Linkage
Disequilibrium
(Indirect)
Linkage
Allelic Association
(Direct)
Type of Association
w/i Family between

marker and
phenotype

poly and phenotype
Pop assoc btw

marker and
phenotype
Interpretation
Region implicated
Gene or nearby gene

implicated
Region implicated
Genome-wide
Not now but maybe

in the future
(~60,000)
Now feasible
(~500,000, HapMap)
Resolution
Typically w/i 8-10

centimorgans
recombination
Not relevant

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
(?)
McCarthy, M. I., et al. (2008). Genome-wide association studies for complex

traits: consensus, uncertainty and challenges. Nature Reviews Genetics, 9(5),
356-369.
END OF PRESENTATION
My Friend, Dr. Dan Grupe (~6 5)

Dylan & I are standing on the NEXT level
Yes, from the floor it looked as though Dans head would touch the ceiling
Anx & Dep Assoc of America Annual Meeting 2014
The Case of Height

Thought-experiment:
A sample of 130 000 people would contain 910 cases (tall
folks like Dan)
A casecontrol study of 910 cases and 910 controls for
being tall would have no power to detect any of the
reported findings for height
You would expect to detect none of the variants
contributing to height because of insufficient statistical
power
Small single-nucleotide effects of the kind that can be
detected on SNP chips mandate large samples, but
provide novel insights into the underlying biological
pathways that contribute to trait like individual
Could we run fewer subjects and save money if

we used
a case-control design?
The Case of Height

Thought-experiment:
Taking individuals about 2.5 SDs above the mean (~65
for men), then ~0.7% of the population can be diagnosed
with tallness (99.3% < 65)
The Case of Height

Thought-experiment:
A sample of 130,000 people would contain 910 cases (tall
folks)
A casecontrol study of 910 cases and 910 controls for
Statistically, you would expect to detect none of the
variants owing to insufficient power
provide insights into the underlying biological pathways
that contribute to trait like individual differences in T&P
(N, E, C), intermediate phenotypes (amygdala, ventral
The Case of Height

Thought-experiment:
folks)
Danand
Grupe
A casecontrol study ofLilAlex
910 Big
cases
910 controls for
Statistically, you would expect to detect none of the

variants owing to insufficient power
provide insights into the underlying biological pathways
that contribute to trait like individual differences in T&P
(N, E, C), intermediate phenotypes (amygdala, ventral
The Case of Height

Thought-experiment:
folks like Dan)
A casecontrol study of 910 cases and 910 matched
controls would have no power to detect any of the
reported genetic variants for height
Conclusion: You cannot cut-corners using case-control
designs
Conceptual Roadmap
Individual differences in T&P reflect the brain
e.g., Individuals with higher levels of N/NE
show enhanced activation and slower recovery
in the amygdala
Where do differences in brain activation
come from?
We cant assay tissue from the amygdala in
people, but can we use the genome (DNA) to
identify candidate mechanisms that could be
mechanistically tested in animals?
Students
What are your fundamental questions about th

Nature and Nurture of individual differences in
Temperament and Personality?
What do you want to know?
Charles Darwin

Shackman Psyc210 Module11 NatureNurture Part2

Transféré par

Informations du document

Copyright

Formats disponibles

Partager ce document

Partager ou intégrer le document

Options de partage

Avez-vous trouvé ce document utile ?

Ce contenu est-il inapproprié ?

Droits d'auteur :

Formats disponibles

Shackman Psyc210 Module11 NatureNurture Part2

Transféré par

Droits d'auteur :

Formats disponibles

We wish to suggest a structure for

the salt of deoxyribonucleic

we should remain unabashed about the

Plan for Today

Take-home critical thinking

Quick Genetics Primer

What about genes?

- Gene: a region of DNA/RNA sequence, corresponding

- Gene: a region of DNA/RNA sequence, corresponding

- Gene: a region of DNA/RNA sequence, corresponding

- Gene: a region of DNA/RNA sequence, corresponding

Alleles = Individual Differences

Alleles = Individual Differences

Alleles = Individual Differences

Alleles = Individual Differences

SNPs = Individual Differences

SNPs = Individual Differences

How might we try to discover the alleles that predict

Lets start with a

sarstats.net/odds2x2.html (0.90 allele #1 = patients; 0.10 allele #2 = patient; 0.90/0.10 = 9 )

Now we need to scale this up

How the heck are we going to

Details Are Not Important

Details Are Not Important

Details Are Not Important

Fragment of one strand

Details Are Not Important

Fragment of one strand

Binds with complement

Fragment of one strand

Binds with complement

Array of probes for

Details Are Not Important

Fragment of one strand

Binds with complement

Details Are Not Important

Fragment of one strand

Binds with complement

Details Are Not Important

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

Enhance prognosis: You have 3 months to live

Monitor treatment in terms of changes in the underlying neural systems

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

Enhance prognosis: You have 3 months to live

Monitor treatment in terms of changes in the underlying neural systems

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

What is the biological basis of childhood shyness?

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

What is the biological basis of childhood shyness?

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

What is the biological basis of childhood shyness?

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

What is the biological basis of childhood shyness?

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

What is the biological basis of childhood shyness?

Identify at-risk individuals early (e.g., carriers of a particular polymorphism)

What is the biological basis of childhood shyness?

Some Success with GWAS

Some Success with GWAS

Some Success with GWAS

Some Success with GWAS

But theres a potential

The Problem of Small Effects

The Problem of Small Effects