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

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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