Haplotypes When the presence of two or more polymorphisms on a single chromosome is statistically correlated in a population, this is a haplotype Example SNP1, SNP2, and SNP3 occur together 95% of the time DNA SNP1 SNP2 SNP3 a haplotype A haplotype consists of a set of two or more statistically correlated polymorphisms that occur on a single chromosome. An example of a haplotype is shown in the slide. In this case, the SNPs marked SNP1, SNP2, and SNP3 form a haplotype because they occur together 95% of the time. If these each of these SNPs were fairly rare (~1% frequency in the general population) and if they had been completely shuffled by recombination, we would expect them to occur together with a frequency that was a tiny fraction of 1%. Because recombination does not occur uniformly across a chromosome and because it takes many generations to completely shuffle physical markers like SNPs, one should expect haplotypes to occur frequently in a given population. One should also expect the haplotypes inherited in different populations to vary according to the genetic history of that population. Haplotypes should be rarer in older populations where a greater number of recombination events have shuffled the SNPs on a given chromosome. Also, the structure of haplotypes should be different in isolated populations that have experienced a different set of mutations and hence will have haplotypes consisting of different SNPs. In October, 2002 the International HapMap Project was launched to determine the haplotype structure of the human genome. Phase I of this initiative was completed in October, 2005. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

The International HapMap Project Intended benefits To facilitate whole-genome association studies Phase I Goal: 1 SNP / 5kb in 269 individuals from 4 population samples Complete as of October, 2005 Phase II Map additional 4.6 million SNPs in each population sample Ongoing The International HapMap Project is a collaboration of researchers from the United States, Canada, Japan, China, Nigeria, and the United Kingdom. The project focused on four human populations: members of the Yoruba ethnic group from Ibadan, Nigeria, Caucasians from the state of Utah in the United States, members of the Han ethnic group in Beijing, China, and Japanese from Tokyo, Japan. Phase I had the stated goal of genotyping one SNP for every 5kb of DNA sequence in each of the four population samples. This work has been completed and phase II of the project is underway to genotype an additional 4.6 million SNPs in the same populations. The intended benefit of compiling a haplotype map of the human genome is to assist whole-genome association studies of disease genes. Because the SNPs in a haplotype are associated with each other, researchers can pick tagging SNPs that are indicative of a set of haplotypes that suit their purposes. By determining whether the tagging SNP is associated with a disease phenotype, researchers can determine which haplotype region is linked to a disease, thereby greatly facilitating the hunt for disease genes. Determining the haplotype structure of the human genome also allowed the HapMap project to elucidate the structure of blocks of linkage disequilibrium (LD) across the entire human genome. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

A LD map of two human populations From Figure 15 in The International HapMap Consortium (2005) “A haplotype map of the human genome” Nature 437: 1299-1320. Linkage disequilibrium is explained in greater detail in the “Complex Disease Traits” chapter. Briefly put, it measures the degree to which markers like SNPs are associated with each other. When LD is 1, it indicates that a group of markers is always associated with each other. An LD score of zero shows that two or more markers associate with each other at a rate that is no better than chance. The figure in the slide shows a LD map of the human genome based on the Japanese and Han Chinese population samples. All autosomes and the X-chromosome are included. The Y-chromosome is excluded because it does not undergo recombination. Areas of the genome with low LD are indicated by cooler colors while hot colors indicate areas of high LD. The HapMap supported earlier studies that showed that LD is generally higher near the centromeres and lower toward the telomeres. One interesting observation made by the HapMap researchers was that the density and function of genes varied with the degree of LD. Areas with the lowest and highest levels of LD had the greatest density of genes. Genes associated with neurophysiological processes and the immune system were found in areas of low LD, while genes involved in DNA repair, the cell cycle, and RNA metabolism were found in areas of strong LD. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Assessing the power of the HapMap Helped find gene involved in Age-Related Macular Degeneration Using HapMap to find previously described determinants of human gene expression Matched previous results of linkage analysis, ~50% of the time The HapMap has already been used successfully to isolate one of the disease genes responsible for age-related macular degeneration, which is a leading cause of blindness in the developed world. A number of other studies using different approaches have verified these results. Another study used the findings from a linkage analysis of human gene expression phenotypes to determine whether the HapMap could be used to construct an accurate genome-wide association study to find the location of the variants known to be responsible for these phenotypes. In roughly 50% of the cases, the genome-wide association approach confirmed the findings from the earlier linkage analysis. Results such as these suggest that the HapMap should greatly (though not necessarily perfectly) facilitate disease association studies. As SNP maps become denser, the power of the HapMap should increase. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Limitations of the HapMap Not certain what SNP haplotypes will reveal about insertions, deletions, and repetitive elements HapMap database is limited to only four populations More SNPs needed to improve association studies for older human populations While the completion of phase I of the HapMap project should be heralded as a great milestone for the study of genetic disease, there are significant limitations to the power of the HapMap. For example, since the HapMap only makes use of SNPs, it is not clear how these types of polymorphisms will correlate to insertions, deletions, and repetitive elements that are also known to be capable of causing disease. Another limitation is that the phase I HapMap covers only four distinct population groups. It is likely that many haplotypes that are present in other populations may be absent in the current data set. Among these population-specific haplotypes may be some that are associated with diseases. Population history also creates certain problems for the HapMap. Since the human species has its origins in Africa, older human populations, like the Yoruba in the phase I population sample, are likely to have less haplotype structure than populations outside of Africa that passed through genetic bottlenecks during theirs migrations out of that continent. This is reflected in the present HapMap where 75% of the SNPs in the non-African populations are associated with other SNPs, while only 50% are associated in the case of the Yoruba population sample. This suggests that significantly larger number of SNPs will have to be genotyped for the Yoruba to achieve the same level of power in association studies that could presently be done with the non-African population samples. Completion of phase II of the HapMap project will alleviate this problem to some extent. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458