Linkage disequilibrium patterns of the human genome across populations

We studied the patterns of linkage disequilibrium (LD) in the human genome among three populations: African Americans, Caucasians and Ashkenazi Jews. These three populations represent admixed, outbred and isolated populations, respectively. The study examined defined chromosomal regions across the whole genome. We found that SNP allele frequencies are highly correlated between Ashkenazi Jews and Caucasians and somewhat distinct in African Americans. In addition, Ashkenazi Jews have a modest increase in LD compared with Caucasians, and both have greater LD than African Americans. The three populations differed more significantly with regard to haplotype heterogeneity. We found, as expected, that Ashkenazi Jews display the greatest extent of homogeneity and African Americans the greatest extent of heterogeneity. We found that most of the variance in LD can be attributed to the difference between regions and markers rather than to that between different population types. The average recombination rates estimated by low-resolution genetic maps can only explain a small fraction of the variance between regions. We found that LD (in terms of r(2)) decreases as a function of distance even within the so-called 'haplotype blocks'. This has significant consequences when using LD mapping for the genetic dissection of complex traits, as higher density SNP maps will be required to scan the genome.     

Population-specific patterns of linkage disequilibrium in the human 5q31 region

Linkage disequilibrium across the human genome is generally lower in West Africans than Europeans. However in the 5q31 region, which is rich in immune genes, we find significantly more examples of apparent nonrecombination between distant marker pairs in West Africans. Much of this effect is due to SNPs that are absent in Europeans, possibly reflecting recent positive selection in the West African population.     

Functional dimorphism of two hAgRP promoter SNPs in linkage disequilibrium

The agouti related protein (AgRP) exerts its anabolic effects on food intake by antagonising the alpha-melanocyte stimulating hormone (α-MSH) at its receptors, melanocortin receptors 3 and 4 (MC3R and MC4R). A single nucleotide polymorphism (SNP) in the promoter of the human AgRP (hAgRP), –38C>T, was associated with low body fatness. The –38T allele that was associated with low body fatness also resulted in lower promoter activity. Here we report a novel SNP, –3019G>A, again in the promoter of hAgRP, which is in complete linkage disequilibrium (LD) with the –38C>T SNP (linked alleles: –3019A/–38T and –3019G/–38C). Functional analyses in a human adrenal and two mouse hypothalamus cell lines showed that the –3019A allele had significantly higher promoter activity. Hence, the two linked alleles (–3019A and –38T) had opposite effects on promoter function and yet they were both associated with low body fatness. The region encompassing the –38C>T SNP had approximately 1000-fold higher activity than the region encompassing the –3019G>A SNP, potentially determining the net functional effect between these two SNPs.     

Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC

Detailed knowledge of linkage disequilibrium (LD) is regarded as a prerequisite for population-based disease gene mapping. Variable patterns across the human genome are now recognized, both between regions and populations. Here, we demonstrate that LD may also vary within a genomic region in a haplotype-specific manner. In 864 Caucasian unrelated individuals, we describe haplotype-specific LD patterns across the human MHC by the construction of gene-specific allelic haplotypes at 25 loci between HLA-A and Tapasin. Strong and extensive LD is found across both common and rare haplotypes, suggesting that haplotype structure is influenced by factors other than genetic drift, including both selection and differential haplotype recombination. Knowledge of haplotype-specific LD in the HLA may explain the apparent discrepant data from previous studies of global LD, help delineate key areas in mapping HLA-associated diseases and, together with recombination data, provide valuable information about a population's demographic history and the selective pressures operating on it.     

The distribution of linkage disequilibrium over anonymous genome regions

Linkage disequilibrIum (LD), the association of alleles at differentloci, is a powerful tool for genetic mapping and for investigating,at the population level, processes such as recombination, selection,mutation and admixture. Little is known about the distributionof LD across mammalian genomes. Therefore, a survey was undertaken,using microsatellite loci, to evaluate the distribution of LDover several regions of human chromosome 4. Radiation hybrid(RH) and linkage maps provided information on physical and geneticdistances between these lad. A Finnish popu lation sample wasgenotyped using 32 mlcrosateilite lad, and partial marker haplotypeswere determined. Assessment of LD was performed, between allpairs of iocl, using the Fisher's exact test. LD was detectedbetween several loci that were separated by more than 1 Mb or1 cM. Detection of LD was strongly associated with small physicaldistance; its relation to genetic distance was more equivocal.This result may support the hypothesis that linkage maps arerelatively inaccurate over small distances. Our results suggestthat LD is widely distributed in anonymous regions of the humangenome and its use may allow more accurate measurement of smallgenetic distances than does standard linkage analysis. Alternativeexplanations are considered for comparisons in which LD is notdetected between tightly linked loci.     

Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map

Comparison of different metrics, using three large samples of haplotypes from different populations, demonstrates that rho is the most efficient measure of association between pairs of single nucleotide polymorphisms (SNPs). Pairwise data can be modeled, using composite likelihood, to describe the decline in linkage disequilibrium with distance (the Malecot model). The evidence from more isolated populations (Finland, Sardinia) suggests that linkage disequilibrium extends to 427-893 kb but, even in samples representative of large heterogeneous populations, such as CEPH, the extent is 385 kb or greater. This suggests that isolated populations are not essential for linkage disequilibrium mapping of common diseases with SNPs. The in parameter of the Malecot model (recombination and time), evaluated at each SNP, indicates regions of the genome with extensive and less extensive disequilibrium (low and high values of in respectively). When plotted against the physical map, the regions with extensive and less extensive linkage disequilibrium may correspond to recombination cold and hot spots. This is discussed in relation to the Xq25 cytogenetic band and the HFE gene region.     

Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome

The extent of nonrandom association of alleles at two or more loci, termed linkage disequilibrium (LD), can reveal much about population demography, selection, and recombination rate, and is a key consideration when designing association mapping studies. Here, we describe a genome-wide analysis of LD in the zebra finch (Taeniopygia guttata) using 838 single nucleotide polymorphisms and present LD maps for all assembled chromosomes. We found that LD declined with physical distance approximately five times faster on the microchromosomes compared to macrochromosomes. The distribution of LD across individual macrochromosomes also varied in a distinct pattern. In the center of the macrochromosomes there were large blocks of markers, sometimes spanning tens of mega bases, in strong LD whereas on the ends of macrochromosomes LD declined more rapidly. Regions of high LD were not simply the result of suppressed recombination around the centromere and this pattern has not been observed previously in other taxa. We also found evidence that this pattern of LD has remained stable across many generations. The variability in LD between and within chromosomes has important implications for genome wide association studies in birds and for our understanding of the distribution of recombination events and the processes that govern them.Linkage disequilibrium (LD), which refers to the nonrandom association of alleles at two or more loci, plays an important role in evolutionary biology and gene mapping (Coop et al. 2008; Slatkin 2008). LD can reveal much about population demography and, because the extent of LD is approximately inversely proportional to the recombination rate, LD can also uncover variability in recombination rates across genomes and chromosomes (Hedrick 1988; Miyashita and Langley 1988; Daly et al. 2001; Jeffreys et al. 2001; Gabriel et al. 2002; Arnheim et al. 2007). Importantly, LD determines the power and precision of association mapping studies, directly influencing our ability to localize genes and/or loci responsible for traits and diseases (Kruglyak 1999; Weiss and Clark 2002).Studies of LD are dependent on the availability of genomic resources, and across vertebrates comprehensive genome-wide studies have been restricted to model species, in particular mammals. Studies in other organisms, however, are likely to reveal extensive variation in patterns of LD not seen in humans (Slatkin 2008), and organisms with different genomic architecture to mammals may provide novel insight into patterns of LD and genome evolution. Birds are interesting in this respect as most bird genomes are composed of many small (micro) chromosomes and relatively few large (macro) chromosomes. Linkage mapping studies have shown that microchromosomes have a higher recombination rate than their larger counterparts (International Chicken Genome Sequencing Consortium 2004; Stapley et al. 2008). Increased recombination rate is expected to reduce the amount of background LD; however, to date there has been no comprehensive analysis of how LD varies with chromosome length and across macrochromosomes and microchromosomes. With respect to LD in birds, the chicken Gallus gallus has received the most attention; studies have quantified LD in several breeds of domestic chicken but have only focused on relatively few chromosomes (Heifetz et al. 2005; Aerts et al. 2007; Andreescu et al. 2007; Wahlberg et al. 2007; Rao et al. 2008; Abasht et al. 2009). In chickens, LD extends very short distances, which reflects the high recombination rate and relatively large effective population size of domestic fowl relative to other livestock species. Passerines, which make up around half of all birds species, and diverged from chickens at least 80 million yr ago, are beginning to receive attention; however, all studies to date have either investigated single chromosomes (Backström et al. 2006), a few genomic regions (Balakrishnan and Edwards 2008), or have low marker coverage (Li and Merilä 2009).The zebra finch, the second bird to have its genome sequenced, can provide a useful target for a comprehensive LD study. In addition to having the two types of chromosomes (macro- and microchromosomes) characteristic of most birds, the zebra finch genome exhibits an unusual pattern of crossing over. Cytogenetic studies have revealed that the location of meiotic crossover events on the macrochromosomes is highly nonrandom, mostly occurring at the ends of the macrochromosomes (Pigozzi and Solari 2005; Calderón and Pigozzi 2006). This suggests there is a large recombination desert on all macrochromosomes, corresponding with the center of the metacentric chromosomes and the center of the long arm of the acrocentric chromosomes (Calderón and Pigozzi 2006). The suppressed recombination in the middle of the chromosomes is not necessarily related to the position of the centromere, nor to the presence of heterochromatin (Calderón and Pigozzi 2006), which is thought to suppress recombination. It is unknown how stable this pattern of recombination is or if this is characteristic of other zebra finch populations. If it is a persistent phenomenon of zebra finch chromosomes, it is likely to affect the extent of LD across macrochromosomes and generate extensive heterogeneity across and between chromosomes. Interestingly, this pattern has not been reported in chickens (Calderón and Pigozzi 2006; Groenen et al. 2009).Patterns of LD may also co-vary with other sequence features that are correlated with recombination rate, such as heterozygosity, GC content, and the number of genes. Recombination rate is expected to increase heterozygosity (Begun and Aquadro 1992; Nachman 2001), although this pattern may be obscured by the action of other forces such as selection and biased gene conversion (Maynard Smith and Haigh 1974; Ohta 1999). Recombination rate is also positively related to GC content and other sequence features known to co-vary with GC content, e.g., gene density, intron length, CpG motifs (Kong et al. 2002; Meunier and Duret 2004; Groenen et al. 2009). It is unknown how LD and these sequence features will co-vary in the presence of highly nonrandom recombination.The aim of this study was to construct genome-wide LD maps of the zebra finch in order to examine (1) whether LD extended further on macro- than microchromosomes, as predicted by previously described differences in recombination rate; (2) whether LD varied across macrochromosomes, corresponding to the biased location of crossing-over events on chromosome spreads; and (3) whether patterns of LD co-vary with heterozygosity, GC content, and the number of genes; and (4) to assess the stability of patterns in LD, by examining whether contemporary genome-wide variation in recombination rates, as detected by linkage mapping, is consistent with historical recombination rate variation, as inferred from LD maps.     

Ethnic divergence and linkage disequilibrium of novel SNPs in the human NLI-IF gene: evidence of human origin and lack of association with tuberculosis susceptibility

Sequence variation in the human genome has been used as a tool in studying human diseases and the evolutionary history of man. A human inherited predisposition to tuberculosis has been suggested and studied; however, genetic mechanisms are still ambiguous. In the present study, we scanned the regulatory and coding region of Nuclear LIM Interactor-Interacting Factor gene (NLI-IF), which is physically close to the tuberculosis-associated gene NRAMP1. Thirteen biallelic single-nucleotide polymorphisms (SNPs) were identified from four ethnic populations (African–American, Caucasian, Hispanic, and Asian) with population-specific distribution of alleles. The extent of linkage disequilibrium (LD) between 402T>C, and 472−42G>A varied distinctly from complete LD in the non-African–American groups to strong but incomplete LD in African–Americans. Both SNPs were in significant LD with the polymorphism 3′ UTR in NRAMP1 among these ethnic groups (P < 0.02), except 402T>C in African–Americans. In a case-control study with a Caucasian population, three cosmopolitan SNPs (204C>A, 402T>C and 472−42G>A) in NLI-IF showed no significant association with human susceptibility to tuberculosis. Our results support the "out-of-Africa" model of human origin, and suggest the time for the common ancestor dispersing from Africa could not have been more than approximately 385,620 years ago. Received: December 13, 2001 / Accepted: January 8, 2002     

A periodic pattern of SNPs in the human genome

By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing or alignment errors, for example, transposable elements (SINE, LINE, and LTR), tandem repeats, and large duplicated regions. However, we found that the pattern is almost entirely confined to what we define as "periodic DNA." Periodic DNA is a genomic region with a high degree of periodicity in nucleotide usage. It turned out that periodic DNA is mainly small regions (average length 16.9 bp), widely distributed in the genome. Furthermore, periodic DNA has a 1.8 times higher SNP density than the rest of the genome and SNPs inside periodic DNA have a significantly higher genotyping error rate than SNPs outside periodic DNA. Our results suggest that not all SNPs in the human genome are created by independent single nucleotide mutations, and that care should be taken in analysis of SNPs from periodic DNA. The latter may have important consequences for SNP and association studies.     

The impact of SNP density on fine-scale patterns of linkage disequilibrium

Linkage disequilibrium (LD) is a measure of the degree of association between alleles in a population. The detection of disease-causing variants by association with neighbouring single nucleotide polymorphisms (SNPs) depends on the existence of strong LD between them. Previous studies have indicated that the extent of LD is highly variable in different chromosome regions and different populations, demonstrating the importance of genome-wide accurate measurement of LD at high resolution throughout the human genome. A uniform feature of these studies has been the inability to detect LD in regions of low marker density. To investigate the dependence of LD patterns on marker selection we performed a high-resolution study in African-American, Asian and UK Caucasian populations. We selected over 5000 SNPs with an average spacing of approximately 1 SNP per 2 kb after validating ca 12 000 SNPs derived from a dense SNP collection (1 SNP per 0.3 kb on average). Applications of different statistical methods of LD assessment highlight similar areas of high and low LD. However, at high resolution, features such as overall sequence coverage in LD blocks and block boundaries vary substantially with respect to marker density. Model-based linkage disequilibrium unit (LDU) maps appear robust to marker density and consistently influenced by marker allele frequency. The results suggest that very dense marker sets will be required to yield stable views of fine-scale LD in the human genome.     

Human population dispersal "Out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs

Genetic and fossil evidence supports a single, recent (<200,000 yr) origin of modern Homo sapiens in Africa, followed by later population divergence and dispersal across the globe (the "Out of Africa" model). However, there is less agreement on the exact nature of this migration event and dispersal of populations relative to one another. We use the empirically observed genetic correlation structure (or linkage disequilibrium) between 242,000 genome-wide single nucleotide polymorphisms (SNPs) in 17 global populations to reconstruct two key parameters of human evolution: effective population size (N(e)) and population divergence times (T). A linkage disequilibrium (LD)-based approach allows changes in human population size to be traced over time and reveals a substantial reduction in N(e) accompanying the "Out of Africa" exodus as well as the dramatic re-expansion of non-Africans as they spread across the globe. Secondly, two parallel estimates of population divergence times provide clear evidence of population dispersal patterns "Out of Africa" and subsequent dispersal of proto-European and proto-East Asian populations. Estimates of divergence times between European-African and East Asian-African populations are inconsistent with its simplest manifestation: a single dispersal from the continent followed by a split into Western and Eastern Eurasian branches. Rather, population divergence times are consistent with substantial ancient gene flow to the proto-European population after its divergence with proto-East Asians, suggesting distinct, early dispersals of modern H. sapiens from Africa. We use simulated genetic polymorphism data to demonstrate the validity of our conclusions against alternative population demographic scenarios.     

A fine-scale comparison of the human and chimpanzee genomes: linkage, linkage disequilibrium and sequence analysis

We have performed a fine-scale comparative study of the human and chimpanzee genomes, using linkage, linkage disequilibrium and sequence analyses on microsatellite loci spanning a region of approximately 30 cM on human chromosome 4p. Our results extend the findings of previous studies that indicated virtually complete conservation between the human and chimpanzee genomes at the chromosomal and sub-chromosomal level and support the hypothesis, derived from previous analyses of mitochondrial DNA, that chimpanzee populations are more diverse than human ones. By sequencing several human and chimpanzee alleles of two microsatellites we showed that base substitutions that diminish the length of perfect repeats (but do not change allele sizes) are probably responsible for the low heterozygosity of these loci in chimpanzees; our results suggest that the evolutionary history of microsatellites should not be inferred from comparisons of mean allele lengths between populations or species.      

Singleton SNPs in the human genome and implications for genome-wide association studies

The human genome is estimated to contain one single nucleotide polymorphism (SNP) every 300 base pairs. The presence of LD between SNP markers can be used to save genotyping cost via appropriate SNP tagging strategies, whereas absence or low level of LD between markers generally increase genotyping cost. It is quite common that a large proportion of tagging SNPs in a tagging scheme often turn out to be singleton SNPs, that is, SNPs that only tag themselves rather than contribute power to the rest of a region. If genotyping cost is a major concern, which often is the case at the present time for genome-wide association studies, these singleton tagging SNPs would be the primary targets to be removed from genotyping. It is important, however, to understand the characteristics of such SNPs and estimate the impact of removing them in a study. Using the HapMap genotype data and genome wide expression data, we assessed the distribution and functional implications of singleton SNPs in the human genome. Our results demonstrated that SNPs of potentially higher functional importance (eg, nonsynonymous SNPs, SNPs in splicing sites and SNPs in 5' and 3' UTR) are associated with a higher tendency to be singleton SNPs than SNPs in intronic and intergenic regions. We further assessed whether singleton SNPs can be tagged using haplotypes of tagSNPs in the three genome wide chips, that is, GeneChip 500k of Affymetrix, HumanHap300 and HumanHap550 of Illumina, and discussed the general implications on genetic association studies.     

Recombination hotspots and block structure of linkage disequilibrium in the human genome exemplified by detailed analysis of PGM1 on 1p31

The distribution of linkage disequilibrium (LD) in the human genome has important consequences for the design of experiments that infer susceptibility genes for complex disease using association studies. Recent studies have shown a non-random distribution of human meiotic recombination associated with intervening tracts of LD. Little is known about the processes, patterns and frequency of reciprocal meiotic recombination in humans. However, this phenomenon can be better understood by the fine structure analysis of several genomic regions by mapping hotspots and characterizing regions with variable LD. Here, we report clustered hotspot activity with intervening blocks of LD within the human PGM1 gene (1p31) using data derived from meiotic and population studies. Earlier work has suggested a high recombination rate in two regions within the PGM1 gene, site A (exons 4-8) and site B (exons 1A-4). Sequencing of eight individuals across 6 kb of targeted regions in site B identified 18 informative SNPs. Individuals from three distinct populations, Caucasian (n=264), Chinese (n=222) and Vietnamese (n=187), were genotyped, and haplotypes were determined using estimate of haplotypes, ldmax and Arlequin. Allelic association and haplotype analysis in these samples revealed variable recombination rates across PGM1, demonstrating the presence of: (i) three hotspots and (ii) three haplotype blocks. The spatial arrangement of haplotype blocks was identical in all populations studied. The pattern of association within PGM1 represents a region decomposed into small blocks of LD, where increased recombination activity has disrupted the ancestral chromosome. Additionally, crossovers in phased data mapped preferentially to regions where LD collapses, which also overlap with sequence motifs.     

Recent human effective population size estimated from linkage disequilibrium

Effective population size (N(e)) determines the amount of genetic variation, genetic drift, and linkage disequilibrium (LD) in populations. Here, we present the first genome-wide estimates of human effective population size from LD data. Chromosome-specific effective population size was estimated for all autosomes and the X chromosome from estimated LD between SNP pairs <100 kb apart. We account for variation in recombination rate by using coalescent-based estimates of fine-scale recombination rate from one sample and correlating these with LD in an independent sample. Phase I of the HapMap project produced between 18 and 22 million SNP pairs in samples from four populations: Yoruba from Ibadan (YRI), Nigeria; Japanese from Tokyo (JPT); Han Chinese from Beijing (HCB); and residents from Utah with ancestry from northern and western Europe (CEU). For CEU, JPT, and HCB, the estimate of effective population size, adjusted for SNP ascertainment bias, was approximately 3100, whereas the estimate for the YRI was approximately 7500, consistent with the out-of-Africa theory of ancestral human population expansion and concurrent bottlenecks. We show that the decay in LD over distance between SNPs is consistent with recent population growth. The estimates of N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago.     

Extended intermarker linkage disequilibrium in the Afrikaners

In this study we conducted an investigation of the background level of linkage disequilibrium (LD) in the Afrikaner population to evaluate the appropriateness of this genetic isolate for mapping complex traits. We analyzed intermarker LD in 62 nuclear families using microsatellite markers covering extended chromosomal regions. The markers were selected to allow the first direct comparison of long-range LD in the Afrikaners to LD in other demographic groups. Using several statistical measures, we find significant evidence for LD in the Afrikaners extending remarkably over a 6-cM range. In contrast, LD decays significantly beyond 3-cM distances in the other founder and outbred populations examined. This study strongly supports the appropriateness of the Afrikaner population for genome-wide scans that exploit LD to map common, multigenic disorders.