Transcript HGSS Chapters 11 & 12: Modern Gene Hunting (incomplete)

Gene Hunting:
Linkage and Association
We humans are diploid (i.e., we have two copies of a gene), inheriting
one chromosome from mother, the other from father. In transmitting a
chromosome to an offspring, however, the physical process of
recombination (crossing over) results in a chromosome that contains
part of the maternal chromosome and part of the paternal chromosome.
Recombination also makes possible a number of different analytical
strategies in genetics: linkage, ancestry tracing, and some forms of
association.
Key terms: polymorphism, recombination, crossing over, linkage, linkage
analysis, association design, haplotype, linkage equilibrium/disequilibrium,
GWAS (genome-wide association study).
Recombination
(Crossing Over)
In meiosis, homologous
chromosomes join together at a
section and exchange genetic
material.
Homologous chromosomes: chromosomes with the same genes on them. E.g., your
paternal chromosome number 1 and your maternal chromosome number 1.
Recombination:
Linkage
Analysis
Population
Haplotype
Analysis
Ancestry
Tracing
Association
Genome-wide
Association
(Current “Hot”
Technology)
Example:
A a
b B
A a
b B
A a
b B
C c
d D
c C
D d
c C
D d
Key Point about Recombination:
Recombination is a function of
physical distance.
• If two alleles are separated by 8 nucleotides, then
there are “8 chances” of a recombination event
between the two..
• If two alleles are separated by 257 nucleotides,
then then are “257 chances” of a recombination
event between the two.
• Therefore, alleles on the same DNA strand that are
far away are more likely to be broken up by
recombination than alleles that are close together.
Original
Chromosomes:
Allele 1
Allele 2
New
Chromosomes:
Dad
Mom
Pair Up
A
T
C
G
G
C
T
A
G
C
C
T
G
A
C
A
T
T
A
T
T
G
G
C
T
A
G
C
C
T
G
A
C
G
A
T
A
A
T
T
C
T
G
G
G
G
C CC C
T TT T
A AA A
G
G
C
C
C
C
T
T
G
G
A
A
C
C
A
G
T
A
T
T
Exchange
Material
A
T
C
G
G
C
T
A
G
C
C
T
G
A
C
G
A
T
A
T
T
G
G
C
T
A
G
C
C
T
G
A
C
A
T
T
A
T
C
G
G
C
T
A
G
C
C
T
G
A
C
A
T
T
G
C
A
T
C 3 chances
G
G
C
10 chances
T
A
G
C
C
T
G
A
C
A
T
T
G
C
17 chances
In other words:
Alleles close together on the same DNA strand
(i.e., the same chromosome) tend to be transmitted
as a unit.
Alleles far away on the same DNA strand tend to be
broken up.
Definitions:
Linkage: Biological phenomenon that
close to one another tyend to transmitted
as a unit.
Linkage Analysis:
(1) tracing the co-segregation of
(2) one or more marker genes with a
trait gene within pedigrees
(3) within families
Definitions:
Trait gene: A gene that contributes to the
trait of interest, e.g., schizophrenia.
Marker Gene: A polymorphic “gene” with
that does not contribute to the trait but
has a known location in the genome.
Rationale
for Linkage Analysis
Can I predict who gets the disorder (trait)
by knowing the marker genes in a family?
YES: A trait gene is close to a marker.
NO: No trait genes are close to the marker.
Linkage Analysis
A
D
Father’s chromosomes are
aa
Aa
Aa
aa
Aa
a
d
Aa
aa
Aa
aa
Linkage Analysis
A
a
D
d
Father’s chromosomes are
aa
Aa
Aa
aa
Aa
Aa
aa
Aa
aa
Aa
I.1
AA
Aa
Aa
II.1
II.2
II.3
Aa
AA
Aa
III.1
III.2
III.3
aa
aa
I.2
aa
Aa
Aa
II.4
II.5
II.6
II.7
aa
aa
Aa
Aa
III.4
III.5
III.6
III.7
aa
II.8
aa
III.8
Aa
aa
I.1
I.2
D d
d d
A A
Aa
Aa
aa
aa
Aa
Aa
a a
II.1
II.2
II.3
II.4
II.5
II.6
II.7
II.8
A a
AA
A a
aa
a a
Aa
A a
aa
III.1
III.2
III.3
III.4
III.5
III.6
III.7
III.8
d d
d d
D d
d D
d d
d d
d d
d d
d d
d d
d d
d d
D d
D d
d d
d d
Haplotype
Series of alleles along a short
section of the same strand of DNA
DNA Strand:
Haplotype:
ATCTGCCTCGCCATAAAGTCATTCGCTCAT
ATCTGCCTCGCCATAAAGTCATTCGCTGAT
ATCAGCCTCGCCATAAAGTCATTCGCTCAT
ATCAGCCTCGCCATAAAGTCATTCGCTGAT
position 4:
position 28:
T
A
C
G
allele
allele
allele
allele
TC
TG
AC
AG
Linkage Equilibrium
& Disequilibrium
If I know the first allele in a haplotype,
can I predict the second allele?
Yes
Linkage
Disequilibrium
No
Linkage
Equilibrium
Linkage Equilibrium
& Disequilibrium
In other words:
Equilibrium: Frequency of a haplotype is
due to chance.
Disequilibrium: Frequency of a haplotype
differs from chance frequency.
Haplotype
(Graduate)
Chance: If the frequency of allele T is .2
and the frequency of allele C is .4, then the
frequency of haplotype TC is .2*.4 = .08.
Nonchance: If the frequency of allele T
is .2 and the frequency of allele C is .4,
then the frequency of haplotype TC is
significantly different from .08.
Haplotype
(Graduate)
Position 28:
C
G
T
TC
TG
A
AC
AG
Position 4:
Equilibrium
(Graduate)
Position 28:
C
G
T
.08 .12
.2
A
.32 .48
.8
Position 4:
.4
.6
Disequilibrium
(Graduate)
Position 28:
C
G
T
.16 .04
.2
A
.14 .56
.8
Position 4:
.4
.6
Statistics for Equilibrium
(Graduate)
Position 28:
C
G
T X11
X12
p1
A X21
X22
q1
Position 4:
p2
q2
Statistics for Equilibrium
(Graduate)
d = X11X22 - X12X21= cov(L1, L2)
D = X11- p1p2 = X22 - q1q2
If D > 0, D = D/Dmax where Dmax = min(p1q2, p2q1)
If D > 0, D = D/Dmax where Dmax = min(p1p2, q1q2)
R2 = d2 / (p1p2q1q2)
D and R2 are the most often used stats.
Formation of Disequilibrium
(Graduate)
1. Mutation occurs and creates a new spelling variation
(polymorphism).
2. This creates linkage disequilibrium with those polymorphisms along
the same DNA strand with the mutation.
3. Over generations, recombination will break up the disequilibrium with
polymorphisms that are far away from the mutation.
4. Polymorphisms close to the original mutation, however, will remain in
disequilibrium for a longer time.
5. Hence, polymorphisms close to the mutation will be in disequilibrium
longer than polymorphisms farther away from the mutation.
Disequilibrium:
1. Is the norm rather than the exception for short sections of DNA
(100,000 nucleotides).
2. Generates “haplotype blocks” (see next slide).
3. Haplotype Mapping Project (HapMap): provide a map of the
haplotype blocks for the human genome.
4. Allows genome-wide association studies.
Haplotype Blocks:
Section of DNA (vertical bar = polymorphism):
Block 1
Block 2
Block 7
• Haplotype Block: Series of adjacent alleles in strong
disequilibrium.
• Logic: Instead of genotyping all 37 polymorphisms, genotype one in
each block.
• If there is a “hit,” then go back and genotype the other
polymorphisms in that block.
Haplotype block structure
of the cytochrome P450
CYP2C gene cluster on
chromosome 10.
From Walton et al. (2005), Nature Genetics 37, 915-0916.
Association Design
• Begins with KNOWN polymorphism theoretically
expected to be associated with the trait (e.g., DRD2 and
schizophrenia).
• Genotypes people on the gene and phenotypes them on
the trait.
•Tests whether the genotype is associated with the trait.
•Two types:
(1) Population-based (controls = general pop)
(2) Family-based (controls = genetic relatives)
Population-based
Association Design
Genotype:
AA
Aa
Schiz:
Phenotype:
Not Schiz:
Do c2 test for association.
aa
Genome-wide Association Study
(GWAS)
(1) Genotype one locus per haplotype block
(2) Do an association test for every gene.
(3) Number of genes that can be assayed changes
from year to year.
GWAS: Genome-wide
Association Study
1.
DNA arrays with 1,000s of SNPs scattered throughout the genome. (Current
chips in 2009 has1,000, 000 different SNPs)
2.
Select the SNPs so that they cover ALL the genome. (Some DNA chips
concentrate on known protein coding regions rather than trying to cover all
the genome)
3.
Genotype patients and controls on all the SNPs.
4.
Find the SNPs that differ.
5.
Problem: number of statistical tests.
Problems with GWAS
(1) Expensive.
(2) Large number of statistical tests.
(3) Need very, very large samples (10,000 or
more.
Results from GWAS
(1) Good success in medicine.
(2) Limited success for psychiatric disorders
(3) Virtually no success for normal behavioral
traits (personality, IQ)
(4) Genetics of behavior is hyper-polygenic:
many, many, many genes