Dating the Origin of the CCR5-Δ32 AIDS-Resistance Allele by the Coalescence of Haplotypes J....

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  • Slide 1
  • Dating the Origin of the CCR5-32 AIDS-Resistance Allele by the Coalescence of Haplotypes J. Claiborne Stephens, David E. Reich, David B. Goldstein, Hyoung Doo Shin, Michael W. Smith, Mary Carrington, Cheryl Winkler, Gavin A. Huttley, Rando Allikmets, Lynn Schriml, Bernard Gerrard, Michael Malasky, Maria D. Ramos, Susanne Morlot, Maria Tzetis, Carole Oddoux, Francesco S. di Giovine, Georgios Nasioulas, David Chandler, Michael Aseev, Matthew Hanson, Luba Kalaydjieva, Damjan Glavac, Paolo Gasparini, E. Kanavakis, Mireille Claustres, Marios Kambouris, Harry Ostrer, Gordon Duff, Vladislav Baranov, Hiljar Sibul, Andres Metspalu, David Goldman, Nick Martin, David Duffy, Jorg Schmidtke, Xavier Estivill, Stephen J. O Brien, and Michael Dean American Journal of Human Genetics 62:1507 1515, 1998 Presented by: Chad Brock, Lisa Ellison, and Travis Hagey
  • Slide 2
  • Cell Communication One way cells communicate is through receptors. A chemokine receptor is a particular type of protein found in the cell membrane, used by the cell to send and receive chemical messages to/from other cells.
  • Slide 3
  • What HIV Does The CCR5 gene produces the CCR5 chemokine receptor that, with CD4, serves as an entry port for HIV-1 strains that infect white blood cells. HIV attaches to the CCR5 and CD4 proteins of the macrophage cell membrane, inserting its viral DNA into the cell.
  • Slide 4
  • CCR5-32 The CCR5-32 mutation leads to truncation and loss of the receptor on lymphoid cells. Homozygous individuals have nearly complete resistance to HIV-1 infection despite repeated exposure. Heterozygous individuals have delayed onset of AIDS two to three years longer than do CCR5-+/+ individuals
  • Slide 5
  • Frequency of the CCR5-32 Allele in Defined Populations 38 ethnic populations including 4,166 individuals were tested for the CCR5-32 allele (table 1). CCR5-32 deletion High allele frequency among several Caucasian populations Rarity or absence in non-Caucasian populations Led to theory that mutation occurred only once in ancestry of Caucasians, after they migrated out of Africa
  • Slide 6
  • European Distribution of the CCR5-32 Variant A north-to-south cline of allele frequency is affirmed as well as the absence of CCR5-32 among East Asian, Middle Eastern, and American Indian populations. document&doi=10.1371/journal.pbio.0030397
  • Slide 7
  • CCR5-32 Loci on Chromosome 3 The time of origin of the CCR5-32 mutation was estimated on the basis of the persistence of a common ancestral three-locus haplotype among modern CCR5-32-bearing chromosomes. This haplotype includes: CCR5-32 (gene of interest) GAAT (microsatellite) AFMB (microsatellite)
  • Slide 8
  • CCR5 Haplotypes Observed in Modern Caucasians Of the people found to have the CCR5 mutation, 85% are of the haplotype 32-197-215. Thus, the authors suggest that this is the ancestral haplotype. The authors suspect that this haplotype was elevated by natural selective pressures. The estimated time to a common ancestor (time of origin of the 32 mutation) was estimated using coalescent methods based on the modern distribution of derivative 32 haplotypes.
  • Slide 9
  • Microsatellites Microsatellites are repeating sequences in the junk DNA areas. Non-coding (dont code for proteins) Not under selection High rate of mutation
  • Slide 10
  • The authors evaluated seven microsatellites on chromosome 3 for linkage with the CCR5-32 allele. GAAT and AFMB were found to show significant linkage the CCR5-32 allele.
  • Slide 11
  • GAAT has 3 possible alleles: 197 base pairs 193 base pairs 191 base pairs AMFB has 4 possible alleles: 215 base pairs 217 base pairs 219 base pairs 213 base pairs
  • Slide 12
  • N e = 5000 25 years/generation p =.1 (current allele frequency) was either fixed (p=1) or very rare (p=0) -4 N e [ p( ln p) + (1-p) ln (1-p) ] yields 6500 generations 162,500 years ago Since CCR5-32 isnt present in non- caucasian populations, we can assume p was equal to 0, so we can use: p ( ln p) (p 1) [ ] -4Ne-4Ne yields 5100 generations 127,500 years ago Age of mutation under drift
  • Slide 13
  • Age estimation based on haplotype variation In order to estimate the age of the CCR5-32 mutation using the frequency of the ancestral haplotype, the authors first needed estimates for the rates of mutation and recombination. By looking at which alleles are most commonly found with CCR5-32, the authors concluded that the ancestral haplotype for CCR5-32 was GAAT-197 and AFMB-215 (85%)
  • Slide 14
  • r = total rate of change from ancestral haplotype = + c ( = mutation rate) (c = recombination rate) Used previous microsatellite mutation rate estimations from Weber and Wong (1993) =.001 as an upper limit at GAAT and AFMB Age estimation based on haplotype variation Estimation of r
  • Slide 15
  • Age estimation based on haplotype variation Estimation of c Based on wild type haplotype frequencies we able to estimate 1 cM (cemtimorgan recombination distance) is equal to 3.76 cR (centiray physcial distance) Used radiation-hybrid analysis to estimate physical distances for CCR5, GAAT, and AFMB.
  • Slide 16
  • Age estimation based on haplotype variation Estimation of c Used radiation-hybrid analysis to estimate physical distances for CCR5, GAAT, and AFMB. CCR5 is.8 cR from GAAT (.21 cM) GAAT is 2.7 cR from AFMB (.72 cM) cR This means the is a.21% recombination rate between CCR5 and GAAT and.72% recombination between GAAT and AFMB
  • Slide 17
  • Age estimation based on haplotype variation Estimation of c Looking at CCR5-+ (wild type) populations, if recombinations were to occur, 36% of them would result in crossing over with the same haplotype, so 64% of recombinations that occurred inbetween CCR5 and GAAT would result in CCR5 moving next to a different microsatellites. Also, 48% of the wild type haplotypes do not have the 215bp AFMB allele, so 48% of recombinations between GAAT and AFMB would result in a different AFMB allele switching chromosomes. 30.8+1.4+14.4+1.4 = 48
  • Slide 18
  • Age estimation based on haplotype variation Estimation of r Combining these values: c =.64 (.21%) +.48 (.72%) =.005 rate of recombination events which would lead the CCR5-32-197-215 haplotype to transfer the CCR5-32 gene to a different haplotype. r = + c =.001 +.005 =.006 Ignoring mutations in which resulting in changing back to the original haplotype. (very rare)
  • Slide 19
  • Estimation of selection coefficient To estimate the selection pressure to change CCR5-32s frequency from 0 to.1 in G generations: p = p(pw 11 + qw 12 ) w w 11,w 12 and w are dependent on if CCR5- 32 is dominant, codominant, or recessive. If dominant, w 11 = w 12 = 1 w 22 = 1 s w = 1 sq 2 Trial values of s were used until p = 0.1 after G generations of selection. Initial p =.0005 and.0001 (1/2N e if N e = 1,000 and 5,000)
  • Slide 20
  • Estimating the age of CCR- 32 Stephens et al. present an equation to calculate the age of the CCR- 32 mutation based on its level of LD Assuming the mutation was unique, at time zero it will be in complete LD with the alleles at the neighboring loci With an estimate of the rate of recombination between the locus of interest and nearby loci, the age of the mutation may be gauged by the degree of decay of LD In order to do this, the ancestral haplotype has to be identified
  • Slide 21
  • Estimating the ancestral haplotype As alluded to earlier, the authors use the relative frequencies of the different CCR- 32-bearing haplotypes to estimate the ancestral haplotype 32-197-215 is the most common CCR- 32-bearing haplotype (84.8%) and is one mutational step away from the most common non- mutant haplotype, +-197-215 Thus, 32-197-215 was identified as the most likely ancestral haplotype for the CCR- 32 mutation and all other CCR- 32-bearing haplotypes were considered derived
  • Slide 22
  • Calculating the number of generations since the mutation The probability that a given haplotype does not change from its ancestor G generations ago is the following: P = (1-r) G ~ e -rG Solving for G, we get the following: G = -ln(P)/r To estimate P, they use the proportion of observed haplotypes that are ancestral Note: This estimate was originally derived for a dramatically expanding population but also holds for a constant-sized population in which many lineages are highly correlated (extensive periods of coancestry) Variance in estimates of T, however, do depend on tree topology. Why?
  • Slide 23
  • Tree topology and variance in estimates of T
  • Slide 24
  • Calculating G and T Substituting the present frequency of the ancestral haplotype (0.848) for P and the authors estimate of r (0.006) into Equation 2 gives a G = 27.5 generations Assuming a 25-year human-generation time: T = 25*27.5 = 688 Years This calculation, however, assumes the present frequency and r are known without error
  • Slide 25
  • Accounting for uncertainty in parameter estimates The authors note two potential sources of error in their estimates of r and p For r, the regression is consistent with the possibility of a 10%-20% reduction in recombination from their estimate of r in the region where the haplotype resides When they considered lower values