Genomics of Host Defense Against Infectious Disease
Humans are genetically diverse. Genes influence disease susceptibility, immune responses and responses to vaccines and therapy.
Evidence for the heritability of human immune response variation
Identification of genes responsible for immune response variationPrior to genome-wide association studiesUse of genome-wide association studies
Evolutionary biology of human host-pathogen interaction.
Personalized medicine infectious disease (not discussed)
Today’s Lecture:
Heritability of Human Immune Response Variation
Gregersen and Behrens (2006) Nat Rev Genetics 7: 917
Relative Risk of Autoimmune DiseasesAmong Siblings
Genetic Variability of Human Vaccine ResponseIdentical Twin Study
Variations in Antibody Response
Genetic Contribution to Variation
IdenticalNon-Identical
Tan, et al. (2001) Vaccine 19: 2434–2439
Do you think genetics plays a greater role in:
> your risk of dying of cancer OR
> your risk of dying of an infection?
What about Risk of Death by Infection?
Adoptee’s Relative Risk of Death by Same Cause as Biological Parent(Genetics)
Adoptee’s Relative Risk of Death by Same Cause as Adoptive Parent(Environment)
All Causes 1.71Infections 5.81Cardio- and Cerebrovascular 4.52Cancer 1.19
All Causes ~1.0Infections ~1.0Cardio- and Cerebrovascular 3.02Cancer 5.16
Strong Genetic Contribution to the Relative Risk of Death by Infection
Sørensen, et al. (1988) New Engl J Med 318:727
Identification of genes responsible for
immune response variation
Manolio, et al. (2008) J Clin Invest 118: 1590
Genetic and Environmental Contributions toMonogenic and Complex Disorders
Major Genetic Determinant Minor Genetic Determinants
Environmental Determinants
Mendelian and non-Mendelian diseases
• Geneticists have been very successful in discovering the variations due to Mendelian disorders. These are characterized by in that they follow the Mendelian rules of inheritance.
• The study of particular families using linkage studies has been successful for the Mendelian diseases.
• However, the more common complex (i.e. non-Mendelian) disorders have been much more difficult to investigate, even when there are clear genetic components of the disease. Genes contributing to complex traits may be identified by association studies.
Simple Sequence Repeats (SSR): Stretches of 1-6nucleotides repeated in tandem. Slippage of DNApolymerase generates variation in repeat number
Microsatellite: Short tandem repeats that vary innumber among individuals
Common Markers used in Molecular GeneticsCommon Markers used in Molecular Genetics
Single nucleotide polymorphism (SNP): Single basepair differences present in at least 1% of the population
Candidate GeneTrial and error
Genome Wide GenotypingNo prior assumptions
Gene-Marker Relationship
Poland, et al. (2007) Clin Pharm Therap 82: 653
Interplay between Innate and AcquiredImmune Responses to Measles
Examples of Genes Affecting Infectious DiseaseSusceptibility and Resistance
TLR Polymorphisms
Genes Associated with HIV Susceptibility and Progression
HLA and Viral Disease Susceptibility
LPS, LipopolysaccharideLTA, Lipoteichoic Acid, LTAPG, Peptidoglycan, PGTLRs, Toll Like ReceptorsNLRs, Nucleotide Binding
Oligomerization Like ReceptorsMyD88, Myeloid Differentiation
Antigen 88, MyD88
Toll Like Receptor Signaling
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Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542
Mutations Affecting Innate Immunity
TLR Polymorphisms and Disease
Misch and Hawn (2008) Clinical Science 114: 347-360
Genetic Influences on HIV Susceptibility and Progression
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HLA Associations with Viral Infections
Martin and Carrington (2005) Current Opinion in Immunology 17: 510516
A, B & C, Class I, Cytotoxic T cellsD, Class II, Helper T cells
Mapping Genetic TraitsBy Genome-Wide Association
Requires:
- Large numbers of genetic markers to cover genome
- Methods to extensively genotype large numbers of people
Genetic Linkage and Association
Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542
How many SNPs?
Nickerson and Kruglyak, Nature Genetics, 2001
~ 10 million common SNPs (> 1- 5% MAF) - 1/300 bp
Common Genotyping Strategies
Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542
Golden Gate Genotyping (Ilumina, Inc.)Golden Gate Genotyping (Ilumina, Inc.)
Allele-Specific Ligation….Primer Hybridization
to Amplified Genomic DNA
Allows Amplification with One of Two Universal Fluorescent Primer Pairs
Gene-Specific Tags
Direct HybridizationTo Gene-Specific Spots
On Microarray Beads
International HapMap project
Feb 2001 - 1.42 million (1/1900 bp)Nov 2003 - 2.0 million (1/1500 bp)Feb 2004 - 3.3 million (1/900 bp)Mar 2005 - 5.0 million (validated - 1/600 bp)
• Provide a collection of millions of SNPs spanning the genome, and serving as genetic markers.
• Study correlations in the inheritance of SNPs (linkage disequilibrium, LD)
• Characterize haplotype blocks• Provide a guide for whole genome association studies
Haplotypes and Tag SNPs
In theroy, 6 SNPs would distinguish 26 = 64 different haplotypes, if each is inherited independently of the others. However in this example, just 4 haplotypes comprise 90% of the observed chromosomes. This indicates the presence of linkage disequilibrium.
The SNPs fall into 2 groups (SNPs 1, 2 & 3 and SNPs 4, 5 & 6) such that by knowing nucleotide of any one of the SNPs (known as a Tag SNP) one can predict the sequences of the other SNPs in the group. The use of Tag SNPs and linkage disequilibrium reduces the number of SNPs required for genome-wide association mapping studies.
Linkage equilibrium: Loci Aa and Bb are in equilibriumif their transmission probabilities πA and πB are independent
Linkage disequilibrium: Loci linked in transmission, i.e. that are inherited together.
πAB πA πB=
r 2 =(πAB - πA πB )πA πB πa πb
Linkage DisequilibriumLinkage Disequilibrium
Haplotype Blocks
Recombination Hotspots are Widespread and Account for LD Structure
Recombination Hot SpotsSNPs
Ancestral DNA
Non-ancestral DNA
Loss of Linkage (Linkage Disequilibrium) Around a Mutation
Low LD
High LD
Distance kB
R2
LD Usually does not Extend Beyond 100 kB
Genome-Wide Scan for Allele Frequency Differences Between 2 Control Groups
P values SNP allele frequencies
Test Statistics
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Genome-Wide Scan for Allele Frequency Differences By Geographic Region
Wellcome Trust Case Control Consortium (2007) Nature 447: 661
Illustrates Stratification
Example of Chromosome Region withStrong Evidence of Geographic Association
Wellcome Trust Case Control Consortium (2007) Nature 447: 661
Geographic Bias may Still be Interesting
Genome-Wide Scan for Allele Frequency Differences Associated with Seven Diseases
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Examples of Chromosome Regions withStrong Evidence of Disease Association
Note effect of recombination on SNP associationWellcome Trust Case Control Consortium (2007) Nature 447: 661
Genome Regions with Strongest Disease AssociationsOdds Ratio
Wellcome Trust Case Control Consortium (2007) Nature 447: 661
GW Association: AdmixureH
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Genome-Wide SNP Associations with Gene Expression Variation
Genes frequently display variations in expression levels among individuals
Much of the variation is linked to statistically significant associations with SNPs
Most associated SNPs are linked to the differentially expressed gene itself (cis-effects)
Modest differences in gene expression (20%) can be associated with individual SNP alleles.
R2 values for single allele effects on gene expression range from 0.2 to 0.6.
Variations in gene expression also results from sequence copy number variation as assessed by comparative genomic hybridization.
Stranger et al., (2005) Plos Genetics 1: e78
Stranger et al. (2007); Science 315: 848.
Cheung et al. (2005); Nature 437: 1365.
SNP Mapping of Gene Expression Variation
Genome AnnotationGene modelsSequence elementsChIP on Chip (Histone Acetyl., etc)
Haplotype Block
Expression
Evolutionary Genomics
Epidemic Disease inNew World Following
European ContactMortality from infectious disease (e.g. smallpox, measles, influenza, etc.) contributing to declines of 80-95% among indigenous peoples.
The concept of innate susceptibility is controversial due to complex interplay among genetic, epidemiologic, and socio-environmental factors and difficulties estimating pre-contact population sizes. Academic jealousies, politics and turf wars add to the fun.
Innate susceptibility implies rapid evolution between the time of common ancestry and renewed contact (10- 20,000 years).
Brazilian Shaman, 1578. Noble David Cook. Born to Die. Cambridge University Press, 1998, page 119.
Recent Acceleration of HumanAdaptive Evolution
High Linkage DisequilibriumAround Selected Alleles
Age Distribution of Ascertained Selected Alleles
Wang E. T. et.al. PNAS 2006;103:135-140 Hawks J. et.al. PNAS 2007;104: 2053-2058
Lethal Response to 1918 Flu
Loo and Gale (2007) Nature 445: 267
In such cases, strong selectionagainst immune responses