PowerPoint PresentationMapping genes contributing to complex diseasesMS susceptibility genes are difficult to mapLinkage vs Association studiesLinkage disequilibriumCase-control studies in genetic epidemiologyThe transmission-disequilibrium testSlide 8Haplotype mappingSlide 10Exercises on LDMapping MS genes in TasmaniaSlide 13Tasmanian Population GrowthSlide 15Slide 16What might have happened in the population?Design of the Tasmanian MS studyWhat strategy could be used to map MS susceptibility genes in Tasmania?MS study in Tasmania: designAnalysis optionsFirst mathematical questionsAverage length of shared chromosomal segmentsNature and numbr of relatives needed to give accurate haplotypesReconstructing haplotypes from genotypesGenotyping1Genes and MS in Tasmania, cont. Lecture 5, Statistics 246February 3, 2004Mapping genes contributing to complex diseases3MS susceptibility genes are difficult to map MS is a complex disease. Analyses with traditional methods such as single marker association studies and standard linkage approaches (affected sib-pairs, pedigrees etc) have failed to agree on genomic regions other than the HLA region.There are a variety of possible reasons for this: •Allelic and locus heterogeneity (no single gene model fits all)•Significant environmental influences•Imprecise phenotyping4Linkage vs Association studies•Linkage mapping: tests for cosegregation of a marker allele with the disease within families•Association mapping: seeks a marker allele that is present more frequently in cases than in controls; all affected individuals are treated as distant relatives–Case/control studies–Transmission disequilibrium test (needs triads)We will do a quick review of association mapping before turning to our MS study.5Linkage disequilibrium Suppose that we have a marker with just two alleles, M and m say, having frequencies p and 1-p, and a (not necessarily linked) disease locus with alleles D and d, having frequencies q and 1-q. A (haploid) gamete must have one of the four combinations (haplotypes) DM, Dm, dM or dm. Let the frequencies in a population of these four haplotypes be x1, x2, x3 and x4 . Under independence, we would have x1 = pq, etc. Deviations of the observed haplotype frequencies from these products is termed linkage disequilibrium (LD), or, better, gametic association. If inheriting the allele D at the disease locus increases the chance of getting the disease, and the disease and marker loci are in LD, then the frequencies of the marker alleles M and m will differ between diseased and non-diseased individuals. This observation is the basis of association studies.6Case-control studies in genetic epidemiology Case-control studies compare case and control allele frequencies at markers or candidate genes (the “exposure” variables). All the standard potential drawbacks of such studies apply, with the similarity of the two base populations being the most critical here. It is thought to be relatively easy for samples from racially mixed populations to differ in allele frequencies, and hard to deal with this in the genetic context. Key term: population structure. If our cases are MS patients, who are our controls? It would be rare for a study to be able to afford or get ethics approval to carry out random sampling of the relevant background population. More commonly, controls are people such as blood donors, whose blood (DNA) has been collected for other purposes. How close will they be to a random sample from the case population? In an effort to deal with this, the TDT which follows in effect uses untransmitted genotypes as controls, bypassing any population structure.7The transmission-disequilibrium test The TDT, as it is called, in its simplest form, starts with parents and an affected child, and considers a biallelic marker locus at which all three are typed, and we can determine which maternal and paternal alleles were transmitted, and which were not. For example, if the parents were a1/a2 and a1/a1 , and the affected offspring was a1/a2 , then a2 was transmitted and a1 was not transmitted by the first parent. From a random sample of such trios (called triads), a 22 table can be built up giving the number of times a1 and a2 were transmitted and were not transmitted, respectively, and a simple test can be derived. Many generalizations of this procedure now exist, see notes for Stat 260, 1998 Week 5.82 136191517419629 172 121271467118 181410 10Genotypes Haplotypes131154921712761184102691716921214718110HaplotypeRe-construction• A collection of alleles derived from the same chromosomeWhat is a haplotype?Chromosome phase is knownChromosome phase is unknown9Haplotype mapping If alleles at a disease locus are associated with alleles at one nearby marker locus on gametes, they are likely to be associated with alleles at other nearby marker loci, and hence with marker haplotypes. A potentially more powerful way to locate disease genes is to search for associations between marker haplotypes and disease. There are two possible problems here stemming from the fact that there can be a very large number of marker haplotypes: we may have to deal with very small frequencies, and we have a multiple testing problem.10 Searching for common or rare haplotypes in cases alone is one form of association mapping. It has been successful, as very substantial LD can arise around disease loci. In general controls are necessary as the background LD can be large. That is, there can be substantial LD between putative disease gene alleles and alleles of nearby markers, without there being any causal link between the gene and the disease. We call this background LD. Background LD can be large –when the population is young–when the # of founders is small (bottlenecks)–through admixture of populations LD, haplotype mapping and background LD11Exercises on LD1. Under a random mating assumption, the long term values of the frequencies x1, x2, x3 and x4 on page 5 above are pq, (1-p)q, p(1-q) and (1-p)(1-q). (Week 5, Stat 260, 1998). 2. Demonstrate that a mixture (e.g. 50:50) of two populations initially in linkage equilibrium at two loci, will typically not be in LE.3. Explain why a single mutant arising by chance, will initially be in strong LD with alleles at loci near the locus on which it arises.Mapping MS genes in Tasmania13 Area: 67,800 km2 Population: 470,000Tasmania Capital city: Hobart
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