Gene Hunting: Linkage and Association

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Gene HuntingLinkage 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/disequilibr
ium, GWAS (genome-wide association study).
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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., yourpaternal chromosome
number 1 and your maternal chromosome number 1.
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Recombination
PopulationHaplotypeAnalysis
LinkageAnalysis
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Example
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Key Point about Recombination
Recombination is a function ofphysical 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.

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In other words
Alleles close together on the same DNA
strand(i.e., the same chromosome) tend to be
transmittedas a unit.Alleles far away on the
same DNA strand tend to bebroken up.
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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
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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.
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Rationalefor 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.
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Fathers chromosomes are
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Haplotype
Series of alleles along a short section of the
same strand of DNA
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Linkage Equilibrium Disequilibrium
In other words
Equilibrium Frequency of a haplotype is due to
chance.
Disequilibrium Frequency of a haplotype
differs from chance frequency.
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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.
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Haplotype
(Graduate)
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Equilibrium
(Graduate)
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Disequilibrium
(Graduate)
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Statistics for Equilibrium (Graduate)
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Statistics for Equilibrium (Graduate)
d X11X22 - X12X21 cov(L1, L2)
D X11- p1p2 X22 - q1q2
If D gt 0, D? D/Dmax where Dmax min(p1q2, p2q1)
If D gt 0, D? D/Dmax where Dmax min(p1p2, q1q2)
R2 d2 / (p1p2q1q2)
D? and R2 are the most often used stats.
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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.

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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.

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Haplotype Blocks
Section of DNA (vertical bar polymorphism)
Block 1
Block 7
Block 2

• Haplotype Block Series of adjacent alleles in
  strongdisequilibrium.
• 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.

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Haplotype block structure of the cytochrome P450
CYP2C gene cluster on chromosome 10.
From Walton et al. (2005), Nature Genetics 37,
915-0916.
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Association Design

• Begins with KNOWN polymorphism
  theoreticallyexpected 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)

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Population-basedAssociation Design
Do c2 test for association.
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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
changesfrom year to year.
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GWAS Genome-wideAssociation 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.

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Problems with GWAS
(1) Expensive.
(2) Large number of statistical tests.
(3) Need very, very large samples (10,000 or
more.
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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