Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region

Recombination, demographic history, drift and selection influence the extent of linkage disequilibrium (LD) in the human genome, but their relative contributions remain unclear. To investigate the effect of meiotic recombination versus population history on LD, three populations with different demographic histories (UK north Europeans, Saami and Zimbabweans) were genotyped for high-frequency single-nucleotide polymorphisms (SNPs) across a 75 kb DNA segment of the MHC class II region. This region spans three well-characterized recombination hotspots and a 60 kb long LD block. Despite a high level of underlying haplotype diversity and considerable divergence in haplotype composition between populations, all three populations showed very similar patterns of LD. Surprisingly, the entire 60 kb LD block was present even in Africans, although it was relatively difficult to detect owing to a systematic deficiency of high frequency SNPs. In contrast, DNA within recombination hotspots did not show this low nucleotide diversity in Africans. Thus, while population history has some influence on LD, our findings suggest that recombination hotspots play a major global role in shaping LD patterns as well as helping to maintain localized SNP diversity in this region of the MHC.     

Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome

A principal goal in human genetics is to provide the tools necessary to enable genome-wide association studies. Extensive information on the distribution of gene-based single-nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD) patterns across the genome is required in order to choose markers for efficient implementation of this approach. To obtain such information, we have genotyped a large Japanese cohort for SNPs identified by systematic resequencing of more than 14 000 autosomal genes. Analysis of these data led to the conclusion that the Japanese population contains approximately 130 000 common autosomal gene haplotypes (frequency >0.05), of which more than 35% are identified in the present study. We also examined allele frequencies and LD patterns according to the position of variants within genes, and their distribution across the genome. We found lower allele variability at exonic SNP sites (both non-synonymous and synonymous) compared with non-exonic SNP sites, and greater average LD between SNPs within exons of the same gene compared with other SNP combinations, both of which could be signals of selection. LD was correlated with the recombination rate per physical distance as estimated from the meiotic map, but the strength of the relationship varied considerably in different regions of the genome. Unique LD patterns, characterized by frequent instances of high LD between non-adjacent SNPs punctuated by blocks of low LD, were found in a 7 Mb region on chromosome 6p that includes the MHC (major histocompatibility complex) locus and many non-MHC genes. These results demonstrate the complexity that must be taken into account when considering SNP variability and LD patterns, while also providing tools necessary for implementation of efficient genome-wide association studies.     

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.     

Antigenic analysis of the major human phosphoglucomutase isozymes:PGM1, PGM2, PGM3 and PGM4

The cross-reactivity of human phosphoglucomutase isozymes (PGMl, PGM2, PGMS and PGM4) has been investigated using anti-rabbit muscle PGM polyclonal antibodies. Significant differepces were revealed: an IgG fraction of the antiserum reacted with the primary and secondary PGMl isozymes of all the common phenotypes. However, there was no reaction with the PGM2 or PGM3 isozymes; thus these latter isozymes share no major antigenic determinants with human or rabbit PGMl and are therefore structurally distinct. In contrast, the PGM isozymes of human milk attributed to a fourth locus, PGM4, showed similar cross-reactivity as PGMl suggesting close structural similarity. The IgG was also employed as a'reagent to remove PGMl from haemolysates so as to allow the unambiguous assessment of the PGMS isozyme patterns by isoelectric focusing. However, no proven genetic variation was encountered in a sample of 32 individuals.     

Comparative study of the haplotype structure and linkage disequilibrium of chromosome 1p36.2 region in the Korean and Japanese populations

The patterns of linkage disequilibrium (LD) in the human genome provide important information for disease gene mapping. LDs may vary depending on chromosomal regions and populations. We have compared LD and haplotypes defined by SNPs in the chromosome 1p36.2 region of the Korean and Japanese populations. Fifty-eight SNPs in about 418 kb ranging from tumor necrosis factor receptor 2 (TNFR2:TNFRSF1B) to procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD) gene were examined in 96 healthy Koreans and Japanese each by direct sequencing and fluorescence correlation spectroscopy combined with the PCR-sequence specific primer method (PCR-SSP-FCS), respectively. Upon pair-wise LD analysis, a total of 25 and 16 out of 58 SNPs greater than MAF 10% were included in LD blocks, encompassing almost 81 kb and 55 kb in total, in Koreans and Japanese, respectively. Both similarities and differences were observed in LD strength and haplotype frequencies between the populations. Considerable similarities were observed in the telomeric region where a long-range block of approximately 80 kb including three genes was found to have strong LDs in both Koreans and Japanese. Significant difference in LD strength was present near the TNFR2 region between the Japanese and Korean populations.     

Complete analysis of HLA-DQB1 polymorphism and DR-DQ linkage disequilibrium by oligonucleotide typing

HLA class II polymorphism is functionally important in the control of immune responses, in transplantation immunology, and in the suceptibility to autoimmune diseases. HLA-DQA1 and -DQB1 genes exhibit a larger degree of allelic polymorphism than usually recognized by routine serology. We have therefore performed an extensive analysis of DQB1 polymorphism by oligotyping. A set of 12 oligo probes was hybridized on polymerase chain reaction-amplified DNA, thus allowing the detection of 12 DQB1 alleles, as demonstrated in homozygous as well as in heterozygous individuals. This highly sensitive detection system is particularly relevant within the DQw1 specificity where the 7 allelic sequences can easily be identified. The DQ-DR linkage disequilibrium was analyzed by oligotyping of 80 Caucasoid heterozygous individuals (160 haplotypes), and very tight associations were observed between DRB1 and DQB1 alleles. Five DRB1 alleles, DR-BON, DR4/Dw4 or Dw14, DR7, DRw8.3, and DRw11, however, can be associated with different DQB1 alleles. Moreover the DRB1 and DQB1 oligotyping analysis performed on 20 randomly chosen DRw8 Caucasoid individuals showed a high prevalence of the DRB1*0801-DQB1*0402 haplotype. By combining the analysis of allelic variations at DRB1, DRB3, and DQB1 loci, we can detect 33 different DR-DQ combinations in our panel of Caucasoid individuals. We now apply DQB1 oligotyping on a routine basis for optimal matching of unrelated donors for bone marrow transplantation.     

Haplotype and linkage disequilibrium analysis of the CRMP1 and EVC genes

In this report, we present the haplotype and linkage disequilibrium (LD) pattern in the Collapsin Response Mediator Protein 1 (CRMP1) and Ellis-van Creveld syndrome (EVC) gene region. We genotyped eight different single nucleotide polymorphisms (SNPs) in the CRMP1 and EVC genes in 90 control individuals of diverse ethnicity. The minor allele frequencies ranged from 3.3-49.4%, with most having a frequency >25%. A total of 37 haplotypes were derived from these eight polymorphisms, with only one haplotype having a frequency >10%. Pairwise LD analysis showed a weak but significant LD between markers located about 243 kb apart in this region. The LD was significant between markers spaced about 208 kb apart in EVC, whereas no LD was found between a pair of markers located about 5 kb apart in CRMP1. However, in general, LD correlated with the distance between loci. The CRMP1 and EVC genes are located near WFS1, the Wolfram syndrome type 1 gene, in which mutations also cause low frequency sensorineural hearing loss (LFSNHL). The haplotypes obtained from these polymorphisms will be useful to track the segregation of phenotypes in families with Ellis-van Creveld syndrome, Weyers acrodental dysostosis, LFSNHL and Wolfram syndrome type 1.     

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.      

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.     

Three-locus haplotype interactions in the analysis of linkage disequilibrium

We have shown that the application of Piazza's formula for the estimation of the "three-locus interaction delta" should not be used for that purpose. In addition, the method of Porta & McHugh, for the demonstration of haplotype interaction in associations between HLA and disease, leads to completely erroneous conclusions. Other methods of calculation that have been used to analyse haplotype interactions also appear to be based on erroneous concepts. We suggest that nothing more than the estimation of heterogeneity in simple 2 X 2 contingency tables should be used for the analysis of linkage disequilibria. This principle is applied to the HLA-A, -B and -C haplotype frequency tables of Baur & Danilovs. For the greater part of the HLA-B alleles, three-locus haplotype frequencies can be explained from the A, B and the B, C disequilibria, without any further haplotype interactions. The predominant exceptions in that respect are haplotypes containing the B44 allele, which has been shown to contain two subgroups and therefore, we are not justified to conclude that this exceptional behaviour of haplotypes with B44 should be attributed to three-locus haplotype interactions.     

Polymorphism of the human retinoid X receptor beta and linkage disequilibrium with HLA-DPB1

The human retinoid X receptor beta (RXRB) gene is localized in the major histocompatibility complex (MHC) region between DPB1 and RING2. The RXRB gene sequence reported by different investigators suggests that the gene may be polymorphic. In this study, we confirmed one polymorphism by sequencing genomic DNA from four Caucasian individuals. We also developed a restriction fragment length polymorphism (RFLP) analysis to detect this specific polymorphism. Linkage analysis studies between RXRB alleles and a number of HLA markers showed significant linkage disequilibrium between RXRB*T and HLA-DPB1*0401.     

Linkage and linkage disequilibrium in chromosome band 1p36 in American Chaldeans with inflammatory bowel disease

The idiopathic inflammatory bowel diseases (IBDs), consisting of Crohn's disease and ulcerative colitis, are complex genetic disorders involving chronic inflammation of the intestines. Multiple genetic loci have been implicated through genome-wide searches, but refinement of localization sufficient to undertake positional cloning efforts has been problematic. This difficulty can be obviated through identification of ancestrally shared regions in genetic isolates, such as the Chaldean population, a Roman Catholic group from Iraq. We analyzed four multiply affected American Chaldean families with inflammatory bowel disease not known to be related. We observed evidence for linkage and linkage disequilibrium in precisely the same region of chromosome band 1p36 reported previously in an outbred population. Maximal evidence for linkage was observed near D1S1597 by multipoint analysis (MLOD = 3.01, P = 6.1 x 10(-5)). A shared haplotype (D1S507 to D1S1628) was observed over 27 cM between two families. There was homozygous sharing of a 5 cM portion of that haplotype in one family and over a <1 cM region in the second family. Homozygous sharing of this haplotype near D1S2697 and D1S3669 was observed in one individual in a third multiply affected family, with heterozygous sharing in a fourth family. Linkage in outbred families as well as in this genetic isolate indicates that a pathophysiologically crucial IBD susceptibility gene is located in 1p36. These findings provide a unique opportunity to refine the localization and identify a major susceptibility gene for a complex genetic disorder.     

Marker-to-marker linkage disequilibrium on chromosomes 5q, 6p, and 8p in Irish high-density schizophrenia pedigrees

Linkage disequilibrium (LD) is a potentially powerful tool for the localization of disease genes for complex disorders. Most prior studies of the relationship between genetic distance and LD have examined only very short distances, focusing on the role of LD in fine-mapping and positional cloning. We examine here the relationship between marker-to-marker (M-M) LD and somewhat greater genetic distances. We analyzed 622 M-M pairings on chromosomes 6p, 8p, and 5q in 265 native Irish pedigrees ascertained for a high density of schizophrenia. LD, significant at the 5% level, was found for 96% of all M-M pairings within 0.5 cM, for 67% within 0.5-1 cM, for 35% within 1-2 cM, for 15% within 2-4 cM, for 8% within 5-10 cM, and for 7% above 10 cM. Thus, in Irish families selected for a high density of schizophrenia, M-M LD may be very common within 0.5 cM and frequent up to distances of 2 cM.     

Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information

The availability of various types of genomic data provides an opportunity to incorporate this data as prior information in genetic association studies. This information includes knowledge of linkage disequilibrium structure as well as which regions are likely to be involved in disease. In this paper, we present an approach for incorporating this information by revisiting how we perform multiple-hypothesis correction. In a traditional association study, in order to correct for multiple-hypothesis testing, the significance threshold at each marker, t, is set to control the total false-positive rate. In our framework, we vary the threshold at each marker t(i) and use these thresholds to incorporate prior information. We present a numerical procedure for solving for thresholds that maximizes association study power using prior information. We also present the results of benchmark simulation experiments using the HapMap data, which demonstrate a significant increase in association study power under this framework. We provide a Web server for performing association studies using our method and provide thresholds optimized for the Affymetrix 500 k and Illumina HumanHap 550 chips and demonstrate the application of our framework to the analysis of the Wellcome Trust Case Control Consortium data.     

Genomic structure of the human tetratricopeptide repeat-containing gene, TTC4, from chromosome region 1p31 and mutation analysis in breast cancers

Loss of heterozygosity (LOH) in 1p31 is a frequent genetic alteration in breast tumors indicating the site of a tumor suppressor gene. We recently isolated a new member of the human tetratricopeptide repeat-containing family of genes, TTC4, which maps to this region. Other members of this gene family have been implicated in tumorigenesis suggesting that TTC4 may represent a breast cancer tumor suppressor gene. We now report the exon/intron structure of TTC4 and single strand conformation polymorphism (SSCP) analysis of DNA from 20 sporadic breast tumors. Although polymorphic variations were identified no mutations affecting the open reading frame of TTC4 were detected. Since the overall region of chromosome 1p31 which undergoes LOH can be relatively large, excluding involvement of newly isolated genes from this region in breast cancer tumorigenesis is an important process for the successful identification of the critical gene. Understanding the structure of TTC4 now makes mutation analysis possible for other cancers and diseases that map to this region.     

Fine mapping of the PTGFR gene to 1p31 region and mutation analysis in human breast cancer

The 1p31 chromosomal region shows loss of heterozygosity (LOH) in up to 50% of human breast cancer, indicating the presence of a tumor suppressor gene at this location. Many efforts have been made to identify candidate genes responsible for breast cancer on the short arm of chromosome 1. It was shown that prostaglandins have been implicated in the tumorigenesis pathway, perhaps via interactions with their cell surface receptors. The prostaglandin F2 receptor gene (PTGFR) was tentatively mapped to 1p31 adjacent to the region undergoing LOH in human breast cancer. We undertook a mutation study in 34 sporadic human breast tumors using a variant of SSCP, incorporation PCR SSCP (IPS). Several nucleotide variants were detected in different tumors. Here we report the nature of these nucleotide changes and the possible involvement of the PTGFR gene in the etiology of human cancer.     

定位人类复杂性状位点的连锁不平衡指数研究进展

随着遗传领域中快速增长的单核苷酸多态性(single nucleotide polymorphism,SNP)和详细的人类单体型数据的获得,群体水平上的连锁不平衡(linkage disequilibrium,LD)定位或关联研究被广泛用来精细定位人类复杂性状位点.一个简单的LD定位方法的关键是选取一个优良的指数来有效地度量性状基因与它紧密相连的遗传标记之间的连锁不平衡程度.本文就精细定位人类复杂性状位点的连锁不平衡指数作一综述.     

Extent and distribution of linkage disequilibrium around the SLC11A1 locus

The SLC11A1 (or NRAMP1) locus on human chromosome 2q35 encodes for the protein solute carrier family 11, member 1. It is expressed in macrophages and involved in the early stages of macrophage priming and activation. Different association studies have shown that the SLC11A1 gene affects susceptibility to infectious diseases and autoimmune inflammatory diseases. Although functional SLC11A1 polymorphisms may account for its role in affecting the susceptibility to these diseases, the positive association can also be because of flanking polymorphisms showing linkage disequilibrium (LD) with this locus. This is the first systematic study to investigate the LD pattern within and around the gene. LD was investigated by genotyping 17 genetic markers in a Chinese population (n=360). The results indicate that LD is maintained at least 110 kb both upstream and downstream of the locus. The complex LD pattern demands that association studies with SLC11A1 should be carried out with both 5' and 3' markers. The strong LD between IL8RB and the 5' SLC11A1 markers also dictates that IL8RB be tested for association with these diseases. Thus, positive association with SLC11A1 should be interpreted cautiously, and IL8RB should also be considered as a potential candidate susceptibility gene unless proven otherwise.