Genomics of Host Defense Against Infectious Disease Humans are genetically diverse. Genes influence disease susceptibility, immune responses and responses to vaccines and therapy. Today’s Lecture: � Evidence for the heritability of human immune response variation � Identification of genes responsible for immune response variation � Prior to genome-wide association studies � Use of genome-wide association studies � Evolutionary biology of human host-pathogen interaction. � Personalized medicine infectious disease (not discussed)
Heritability of Human Immune Response Variation
Relative Risk of Autoimmune Diseases Among Siblings Gregersen and Behrens (2006) Nat Rev Genetics 7: 917
Genetic Variability of Human Vaccine Response Identical Twin Study Variations in Antibody Response Non-Identical Identical Genetic Contribution to Variation Tan, et al. (2001) Vaccine 19: 2434–2439
What about Risk of Death by Infection? Do you think genetics plays a greater role in: > your risk of dying of cancer OR > your risk of dying of an infection?
Strong Genetic Contribution to the Relative Risk of Death by Infection Adoptee’s Relative Risk of Death by Same Cause as Biological Parent (Genetics) All Causes 1.71 Infections 5.81 Cardio- and Cerebrovascular 4.52 Cancer 1.19 Adoptee’s Relative Risk of Death by Same Cause as Adoptive Parent (Environment) All Causes ~1.0 Infections ~1.0 Cardio- and Cerebrovascular 3.02 Cancer 5.16 Sørensen, et al. (1988) New Engl J Med 318:727
Identification of genes responsible for immune response variation
Genetic and Environmental Contributions to Monogenic and Complex Disorders Environmental Determinants Minor Genetic Determinants Major Genetic Determinant Manolio, et al. (2008) J Clin Invest 118: 1590
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 .
Common Markers used in Molecular Genetics Common Markers used in Molecular Genetics Simple Sequence Repeats (SSR): Stretches of 1-6 nucleotides repeated in tandem. Slippage of DNA polymerase generates variation in repeat number Microsatellite: Short tandem repeats that vary in number among individuals Single nucleotide polymorphism (SNP): Single base pair differences present in at least 1% of the population
Gene-Marker Relationship Candidate Gene Genome Wide Genotyping Trial and error No prior assumptions
Interplay between Innate and Acquired Immune Responses to Measles Poland, et al. (2007) Clin Pharm Therap 82: 653
Examples of Genes Affecting Infectious Disease Susceptibility and Resistance TLR Polymorphisms Genes Associated with HIV Susceptibility and Progression HLA and Viral Disease Susceptibility
Toll Like Receptor Signaling Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542 LPS, Lipopolysaccharide LTA, Lipoteichoic Acid, LTA PG, Peptidoglycan, PG TLRs, Toll Like Receptors NLRs, Nucleotide Binding Oligomerization Like Receptors MyD88, Myeloid Differentiation Antigen 88, MyD88
Mutations Affecting Innate Immunity Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542
TLR Polymorphisms and Disease Misch and Hawn (2008) Clinical Science 114: 347-360
Genetic Influences on HIV Susceptibility and Progression Telenti and U. M. Zanger Annu. Rev. Pharmacol. Toxicol. 2008. 48:227-256
HLA Associations with Viral Infections A, B & C, Class I, Cytotoxic T cells D, Class II, Helper T cells Martin and Carrington (2005) Current Opinion in Immunology 17: 510516
Mapping Genetic Traits By 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 Gene-Specific Tags Direct Hybridization To Gene-Specific Spots On Microarray Beads Allows Amplification with One of Two Universal Fluorescent Primer Pairs
International HapMap project • 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 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)
Haplotypes and Tag SNPs In theroy, 6 SNPs would distinguish 2 6 = 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 Disequilibrium Linkage Disequilibrium Linkage equilibrium: Loci Aa and Bb are in equilibrium if their transmission probabilities π A and π B are independent π AB π A π B = Linkage disequilibrium: Loci linked in transmission, i.e. that are inherited together. (π AB - π A π B ) r 2 = π A π B π a π b
Haplotype Blocks
Recombination Hotspots are Widespread and Account for LD Structure Recombination Hot Spots SNPs
Loss of Linkage (Linkage Disequilibrium) Around a Mutation Ancestral DNA Non-ancestral DNA Low LD High LD
LD Usually does not Extend Beyond 100 kB R 2 Distance kB
Genome-Wide Scan for Allele Frequency Differences Between 2 Control Groups P values SNP allele frequencies Wellcome Trust Case Control Consortium (2007) Nature 447: 661 Test Statistics
Genome-Wide Scan for Allele Frequency Differences By Geographic Region Illustrates Stratification Wellcome Trust Case Control Consortium (2007) Nature 447: 661
Wellcome Trust Case Control Consortium (2007) Nature 447: 661 Example of Chromosome Region with Strong Evidence of Geographic Association Geographic Bias may Still be Interesting
Genome-Wide Scan for Allele Frequency Differences Associated with Seven Diseases Wellcome Trust Case Control Consortium (2007) Nature 447: 661
Examples of Chromosome Regions with Strong Evidence of Disease Association Note effect of recombination on SNP association Wellcome Trust Case Control Consortium (2007) Nature 447: 661
Genome Regions with Strongest Disease Associations Odds Ratio Wellcome Trust Case Control Consortium (2007) Nature 447: 661
GW Association: Admixure Hafler and Dejager (2005) Nat Rev Immunol 5: 83
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. � R 2 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. (2007); Science 315: 848 Cheung et al. (2005); Nature 437: 1365 . . Stranger et al., (2005) Plos Genetics 1: e78
Expression SNP Mapping of Gene Expression Variation Genome Annotation � Gene models � Sequence elements � ChIP on Chip (Histone Acetyl., etc) Haplotype Block
Evolutionary Genomics
Epidemic Disease in New World Following European Contact Mortality 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.
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