Statistical Issues in Human Genetics

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Statistical Issuesin Human Genetics

• Jonathan L. Haines Ph.D.
• Center for Human Genetics Research
• Vanderbilt University Medical Center

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COMMON COMPLEX DISEASE
Environment
Genes
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COMMON COMPLEX DISEASE
Environment
Genes
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What Can The Genes Tell Us?

• Give us a better understanding of the underlying
  biology of the trait in question
• Serve as direct targets for better treatments
• Pharmacogenetics
• Interventions
• Give us better predictions of who might develop
  disease
• Give us better predictions of the course of the
  disease
• Lead to knowledge that can help find a cure or
  prevention

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• Watson and Crick started it all in 1953 with the
  description of DNA
• 53 Year Anniversary of the paper will be in
  April.
• Both Won Nobel Prize

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The DNA Between Individuals is Identical. All
differences are in the 0.1 of DNA that varies.
A C C G T C C A G G
A C C G T G C A G G
Its hard to believe sometimes!
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HUMAN CHROMOSOMES
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Single-Nucleotide Polymorphisms (SNPs)One of the
most common types of variation
GATCCTGTAGCT
1st Chromosome
GATCCTCTAGCT
2nd Chromosome
G/C
Affected
Normal
GATCCTGTAGCT
GATCCTCTAGCT
GATCCTGTAGCT
GATCCTCTAGCT
Extremely frequent across the genome (1/400 bp)
- high resolution
Easy to genotype - high-throughput techniques
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What are We Looking For?
Earth
City
Street
Address
Human Genome
Chromosome
Gene (DNA)
Band
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640 cubic yards
3,000 MB
1/100 cubic inch
1 x 10-6 MB
It really is like finding a needle in a
haystack! (and a very BIG haystack, at that)
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The Genome Sequence is not THE answer!
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Disease Gene Discovery In Complex Disease
1. Define Phenotype a. Consistency b.
Accuracy
2. Define the Genetic Component a. Twin Studies
b. Adoption Studies c. Family Studies
d. Heritability e. Segregation Analysis
3. Define Experimental Design
4. Ascertain Families a. Case-Control b.
Singleton c. Sib Pairs d. Affected
Relative Pairs
5. Collect Data a. Family Histories b.
Clinical Results c. Risk Factors d. DNA
Samples
6. Perform Genotype Generation a. Genomic
Screen b. Candidate Gene
7. Analyze data
c. Association studies
case-control, family-based
b. Model-independent sib-pair, relative pair
a. Model-dependent Lod score
8. Identify, Test, and Localize Regions of
Interest
9. Bioinformatics and Gene Identification
10. Identify Susceptibility Variation(s)
11. Define Interactions a. Gene-Gene b.
Gene-Environment
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CLASSES OF HUMANGENETIC DISEASE

• Diseases of Simple Genetic Architecture
• Can tell how trait is passed in a family follows
  a recognizable pattern
• One gene per family
• Often called Mendelian disease
• Usually quite rare in population
• Causative gene
• Diseases of Complex Genetic Architecture
• No clear pattern of inheritance
• Moderate to strong evidence of being inherited
• Common in population cancer, heart disease,
  dementia etc.
• Involves many genes or genes and environment
• Susceptibility genes

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CLASSES OF HUMANGENETIC DISEASE

• Diseases of Simple Genetic Architecture
• Can tell how trait is passed in a family follows
  a recognizable pattern
• One gene per family
• Often called Mendelian disease
• Usually quite rare in population
• Causative gene
• Diseases of Complex Genetic Architecture
• No clear pattern of inheritance
• Moderate to strong evidence of being inherited
• Common in population cancer, heart disease,
  dementia etc.
• Involves many genes or genes and environment
• Susceptibility genes

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Modes of Inheritance

• Autosomal Dominant
• Huntington disease
• Autosomal Recessive
• Cystic fibrosis
• X-linked
• Duchenne muscular dystrophy
• Mitochondrial
• Leber Optic atrophy
• Additive
• HLA-DR in multiple sclerosis
• Combinations of the above
• RP (39 loci), Nonsyndromic deafness

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Linkage Analysis

• Traces the segregation of the trait through a
  family
• Traces the segregation of the chromosomes through
  a family
• Statistically measures the correlation of the
  segregation of the trait with the segregation of
  the chromosome

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A SAMPLE PEDIGREE
The RED chromosome is key
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Measures of LinkageParametric Vs Non-Parametric

• Two major approaches toward linkage analysis
• Parametric Defines a genetic model of the
  action of the trait locus (loci). This allows
  more complete use of the available data
  (inheritance patterns and phenotype information).
• The historical approach towards linkage analysis.
  Development driven by need to map simple
  Mendelian diseases
• Quite powerful when model is correctly defined
• Non-Parametric Uses either a partial genetic
  model or no genetic model. Relies on estimates
  of allele/ haplotype/region sharing across
  relatives. Makes far fewer assumptions about the
  action of the underlying trait locus(loci).

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Linkage Analysis

• Families
• Affected sibpairs
• Affected relative pairs
• Extended families
• Traits
• Qualitative (affected or not)
• Quantitative (ordinal, continuous)
• There are numerous different methods that can be
  applied
• These methods differ dramatically depending on
  the types of families and traits

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Recombination Natures way of making new
combinations of genetic variants
A. B.
C. D.
A. A diploid cell. B. DNA replication and
pairing of homologous chromosomes to form
bivalent. C. Chiasma are formed between the
chromatids of homologous chromosomes D.
Recombination is complete by the end of prophase
I.
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Linkage Analysis in Humans

• Measure the rate of recombination between two or
  more loci on a chromosome
• Can be done with any loci, but primary
  application is to find the location of a trait
  variant by measuring linkage to known marker
  variants.

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LOD Score Analysis
The likelihood ratio as defined by Morton
(1955) L(pedigree? x)
L(pedigree ? 0.50) where ?
represents the recombination fraction and where 0
? x ? 0.49. When all meioses are scorable,
the LR is constructed as L.R.
z(?) is the lod score at a particular value of
the recombination fraction z(?) is the maximum
lod score, which occurs at the MLE of the
recombination fraction
?
The LOD score (z) is the log10 (L.R.)
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CLASSES OF HUMANGENETIC DISEASE

• Diseases of Simple Genetic Architecture
• Can tell how trait is passed in a family follows
  a recognizable pattern
• One gene per family
• Often called Mendelian disease
• Usually quite rare in population
• Causative gene
• Diseases of Complex Genetic Architecture
• No clear pattern of inheritance
• Moderate to strong evidence of being inherited
• Common in population cancer, heart disease,
  dementia etc.
• Involves many genes or genes and environment
• Susceptibility genes

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Study Designs
Linkage Analysis
Large Families
Small Families
Association Studies
Family-Based
Case-Control
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Linkage vs. Association
Linkage
Association
Shared within Families
Shared across Families
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TESTING CANDIDATE GENES
Disease
Normal
5/20
5/20
Gene is not important
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TESTING CANDIDATE GENES
Disease
Normal
10/20
5/20
Gene may be important
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Two Basic Study Designsfor Association Analysis

• Case-Control
• Advantages
• Power
• Ascertainment
• Disadvantages
• Sensitivity to assumptions
• Matching

• Family-Based
• Parent-child Trio
• Discordant sibpairs
• Advantages
• Use existing samples
• Robustness to assumptions
• Disadvantages
• Ascertainment
• Power

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METHODS FOR FAMILY-BASED ASSOCIATION STUDIES

• Sibship
• SDT
• WSDT
• FBAT
• Pedigree
• Transmit
• PDT
• FBAT

• Parent-Child
• AFBAC
• TDT
• HHRR
• QTDT
• Sibpair
• S-TDT
• DAT

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TRANSMISSION DISEQUILIBRIUM TEST (TDT)

• Examines transmission of alleles to affected
  individuals
• Requires
• Linkage (transmission through meioses) and
• Association (specific alleles)
• Test of linkage if association assumed
• Test of association if linkage assumed
• Test of linkage AND association if neither
  assumed
• Uses the non-transmitted alleles, effectively, as
  the control group. Can make pseudocontrol by
  creating genotype of the two non-transmitted
  alleles
• Requires phenotype only for the child

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TDT calculation
Transmitted
2
1
12
12
Non-Transmitted
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With 5 per cell, this follows a ?2 distribution
with 1 df
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TDT
12
12
Transmitted
1 2 Not
transmitted 1 0 0
2 2 0
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TDT
22
12
Transmitted
1 2 Not
transmitted 1 0 0
2 1 1
12
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TDT
22
11
Transmitted
1 2 Not
transmitted 1 1 0
2 0 1
12
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TDT Example
Transmitted
Transmitted
2
1
2
1
Non-Transmitted
Non-Transmitted
(42-25)2
4.31
TDT
(4225)
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Two Basic Study Designsfor Association Analysis

• Case-Control
• Advantages
• Power
• Ascertainment
• Disadvantages
• Sensitivity to assumptions
• Matching

• Family-Based
• Parent-child Trio
• Discordant sibpairs
• Advantages
• Use existing samples
• Robustness to assumptions
• Disadvantages
• Ascertainment
• Power

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Analysis of Case-Control Data

• Standard epidemiological approaches can be used
• Qualitative trait
• Logistic regression
• Quantitative trait
• Linear regression
• The usual concerns about matching but must also
  worry about false-positives from population
  substructure

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Incorporating Geneticsinto Your Studies

• Obtain appropriate IRB approval
• DNA studies are quite common
• Template language exists for IRB approval and
  consent forms
• Genetic Studies Ascertainment Core (GSAC) can
  help
• Kelly Taylor ktaylor_at_chgr.mc.vanderbilt.edu
• Collect family history information
• Obtain DNA sample
• Venipuncture
• Buccal wash/swab
• Finger stick
• Extract/Store DNA
• DNA Resources Core can help
• Cara Sutcliffe cara_at_chgr.mc.vanderbilt.edu
• http//chgr.mc.vanderbilt.edu/

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What Can The Genes Tell Us?

• Give us a better understanding of the underlying
  biology of the trait in question
• Serve as direct targets for better treatments
• Pharmacogenetics
• Interventions
• Give us better predictions of who might develop
  disease
• Give us better predictions of the course of the
  disease
• Lead to knowledge that can help find a cure or
  prevention