Linkage disequilibrium and haplotype analysis among Polish families with spinal muscular atrophy.

Spinal Muscular Atrophy (SMA) is an inherited degenerative disorder of anterior horn cells that results in progressive muscle weakness and atrophy. The autosomal recessive forms of childhood-onset SMA have been mapped to chromosome 5q11.2-13.3, in a number of studies examining different populations. A total of 9 simple sequence repeat markers were genotyped against 32 Polish families with SMA. The markers span an approximately 0.7 cM region defined by the SMA flanking markers D5S435 and MAP1B. Significant linkage disequilibrium (corrected P < .05) was detected at four of these markers, with D/Dmax values of < or = .89. Extended haplotype analysis revealed a predominant haplotype associated with SMA. The apparently high mutation rate of some of the markers has resulted in a number of haplotypes that vary slightly from this predominant haplotype. The predominant haplotype and these closely related patterns represent 25% of the disease chromosomes and none of the nontransmitted parental chromosomes. This predominant haplotype is present both in patients with acute (type I) and in chronic (types II and III) forms of SMA and occurs twice in a homozygous state, both times in children with chronic SMA.     

Linkage disequilibrium between mutation and RFLP haplotype at the phenylalanine hydroxylase locus in the German population

Summary Restriction fragment length polymorphism (RFLP) haplotypes at the phenylalanine hydroxylase (PAH) locus have been determined in 60 German families with PAH deficiency. Similar to the Danish population, about 90% of the mutant alleles are confined to four distinct haplotypes. There are however, differences in the frequency distributiion of these haplotypes among the mutant alleles between the two populations. Using an oligonucleotide probe for the splicing mutation associated with mutant haplotype 3 in the Danish population, a tight association between the mutation and the RFLP haplotype has also been observed in Germany. The results provide strong evidence that the splicing mutation occurred on a haplotype 3 chromosome and that the mutant allele has spread into different populations smong Caucasians.     

Linkage disequilibrium between RFLP haplotype 2 and the affected PAH allele in PKU families from the Berlin area of the German Democratic Republic

Summary Probands from 26 PKU-affected families of the Berlin area were analyzed with respect to the allele frequency distribution of six RFLPs in linkage with the normal and the PKU alleles of the phenylalanine hydroxylase gene. These investigations confirm most of the RFLP haplotypes observed by Güttler and colleagues in the Danish population and describe two additional ones. They detect no significant differences in the single RFLP or RFLP haplotype distribution on the normal chromosomes in comparison with the Danish families and confirm a prevalent association of the RFLP haplotypes 1,4 and 7 with the normal PAH allele. In contrast to the Danish investigations, in our study the PKU allele is found most frequently linked to haplotype 2, rather then to haplotype 3. In one of our patients we found a substitution of the normal 19-kb MspI fragment by a 13.5- and a 5.5-kb fragment, reported up to now only in one other German family.     

Linkage disequilibrium decay and haplotype block structure in the pig

Linkage disequilibrium (LD) may reveal much about domestication and breed history. An investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total, 371 single-nucleotide-polymorphisms located in three genomic regions were genotyped. The extent of LD differed significantly between European and Chinese breeds, extending up to 2 cM in Europe and up to 0.05 cM in China. In European breeds, LD extended over large haploblocks up to 400 kb, whereas in Chinese breeds the extent of LD was smaller and generally did not exceed 10 kb. The European wild boar showed an intermediate level of LD between Chinese and European breeds. In Europe, the extent of LD also differed according to genomic region. Chinese breeds showed a higher level of haplotype diversity and shared high levels of frequent haplotypes with Large White, Landrace, and Duroc. The extent of LD differs between both centers of pig domestication, being higher in Europe. Two hypotheses can explain these findings. First, the European ancestral stock had a higher level of LD. Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds.     

Spinocerebellar ataxia type 8: molecular genetic comparisons and haplotype analysis of 37 families with ataxia

We reported elsewhere that an untranslated CTG expansion causes the dominantly inherited neurodegenerative disorder spinocerebellar ataxia type 8 (SCA8). SCA8 shows a complex inheritance pattern with extremes of incomplete penetrance, in which often only one or two affected individuals are found in a given family. SCA8 expansions have also been found in control chromosomes, indicating that separate genetic or environmental factors increase disease penetrance among SCA8-expansion-carrying patients with ataxia. We describe the molecular genetic features and disease penetrance of 37 different families with SCA8 ataxia from the United States, Canada, Japan, and Mexico. Haplotype analysis using 17 STR markers spanning an approximately 1-Mb region was performed on the families with ataxia, on a group of expansion carriers in the general population, and on psychiatric patients, to clarify the genetic basis of the reduced penetrance and to investigate whether CTG expansions among different populations share a common ancestral background. Two major ancestrally related haplotypes (A and A') were found among white families with ataxia, normal controls, and patients with major psychosis, indicating a common ancestral origin of both pathogenic and nonpathogenic SCA8 expansions among whites. Two additional and distinct haplotypes were found among a group of Japanese families with ataxia (haplotype B) and a Mexican family with ataxia (haplotype C). Our finding that SCA8 expansions on three independently arising haplotypes are found among patients with ataxia and cosegregate with ataxia when multiple family members are affected further supports the direct role of the CTG expansion in disease pathogenesis.     

Linkage studies of Friedreich ataxia by means of blood-group and protein markers

Friedreich ataxia (FA) is an autosomal recessive, neuro-degenerative disorder in which the pathogenetic mechanism remains unidentified despite extensive biochemical studies. Genetic-linkage studies provide an alternative approach to determining the basic defect. Linkage analysis between FA and 36 polymorphic-blood-group and protein markers has been carried out on three separate patient populations--16 families from the inbred Acadian population of Louisiana, 21 French-Canadian families from Quebec, and nine apparently unrelated British families--in an attempt to determine the chromosomal location of the disease mutation. Neither evidence of linkage to any of the markers investigated nor heterogeneity among the populations was found for any of the comparisons. The negative lod scores exclude the locus for FA from greater than 20% of the genome.     

Linkage disequilibrium and CF allele segregation analysis in cystic fibrosis families in Northern Ireland

Summary Linkage disequilibrium and cystic fibrosis (CF) allele segregation were analysed in 46 CF families in Northern Ireland. The smaller (+) allele of the KM19/PstI polymorphism and the larger (-) allele of the XV-2c/TaqI polymorphism showed marked linkage disequilibrium with CF. This information can be used to alter the risk of an individual being a carrier of CF away from the expected population risk of 1 in 20. The high-risk genotypes K+K+ or X-X- have a risk of 1 in 10 and the low-risk genotypes K-K- or X+X+ have a risk of 1 in 50. A study of the segregation of CF alleles in the 46 families, using KM19 and Xv-2c, showed preferential inheritance of the paternal (79%), as opposed to the maternal (21%), CF allele by the heterozygous carriers. A mechanism that might explain this observation is discussed.     

Linkage disequilibrium and linkage information from one-child families.

In linkage analysis a single-child family is usually considered to be completely uninformative. This article shows that such a family can provide information on linkage disequilibrium, even if it provides no information on linkage equilibrium. A transition matrix consisting of the recombination fraction and the phase proportion is proposed to study the genetic transmission from a pair of parents to their single child. The information about linkage for a single-child family is shown to be confounded by the phase proportion. This explains why such a family used to be considered uninformative under the assumption of linkage equilibrium. By reparametrizing the recombination fraction and the phase proportion into one parameter, it is demonstrated that extracting information on linkage disequilibrium is feasible. The study of power of the testing method proposed here is carried out by simulation.     

Friedreich ataxia in Italian families: Genetic homogeneity and linkage disequilibrium with the marker loci D9S5 and D9S15

Friedreich ataxia (FA) is an autosomal recessive degenerative disease of the nervous system of unknown biochemical cause. The FA gene has been shown to be in close linkage with the two chromosome 9 markers D9S5 and D9S15, and linkage disequilibrium between FA and D9S15 has been detected in French families by Hanauer et al. We used new highly informative markers at the above loci to analyze Italian FA families for linkage and linkage disequilibrium. The new markers were a three-allele BstXI RFLP at D9S5 (PIC = .55) and a six-allele microsatellite, typed by polymerase chain reaction, at D9S15 (PIC = .75). We obtained maximum lod scores of 8.25 between FA and D9S5, 10.55 between FA and D9S15, and 9.52 between D9S5 and D9S15, all at zero recombination. Our results, combined with those reported by other authors, reduce maxlod-1 (maximum lod score minus 1) confidence limits to less than 1.1 cM between FA and D9S5, 1.2 cM between FA and D9S15, and 1.4 cM between D9S5 and D9S15. Linkage disequilibrium with FA was found only for D9S15 when all families were evaluated but was also found for a D9S5/D9S15 haplotype in a subgroup of southern Italian families. We conclude that FA, D9S5, and D9S15 are tightly clustered and that studies of geographically restricted groups may reveal a limited number of mutations responsible for the disease in the Italian population. We present preliminary evidence from pulsed-field gel electrophoresis that D9S5 and D9S15 may be less than 450 kb apart. Linkage disequilibrium between FA and D9S15 suggests that the disease gene may be at an even shorter distance from this marker locus, which therefore represents a very good starting point for cloning attempts.     

Linkage disequilibrium and haplotype mapping of a skin cancer susceptibility locus in outbred mice

Car-R (carcinogenesis-resistant) and Car-S (carcinogenesis-susceptible) outbred mice, obtained by phenotypic selection from an initial intercross of eight inbred strains, show a >100-fold difference in their susceptibility to two-stage skin tumorigenesis. We found that the lines carry a high degree of genetic polymorphism, with an average heterozygosity of 0.39. This polymorphism allowed the use of linkage disequilibrium (LD) and haplotype analysis for the mapping of a skin cancer modifier locus on Chr 7, in a short region of 6 cM, around the Tyr gene. Car-S mice inherited the susceptibility allele at this locus from the A/J, BALB/c, SJL/J, and SWR/J strains. Our results demonstrate the feasibility and usefulness of mapping disease genes by LD in phenotypically selected, genetically heterogeneous animals. Received: 16 March 2000 / Accepted: 9 June 2000     

Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density

OBJECTIVE: Analyze the information contained in homozygous haplotypes detected with high density genotyping. METHODS: We analyze the genotypes of approximately 2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. CONCLUSIONS: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.     

Linkage disequilibrium between phenylketonuria and RFLP haplotype 1 at the phenylalanine hydroxylase locus in Portugal

Summary RFLPs of 36 normal and 41 mutant alleles at the phenylalanine hydroxylase locus were determined in 31 Portuguese kindreds. A total of 14 haplotypes including 10 normal and 7 mutant alleles were observed. Almost 75% of all mutant alleles were confined within only two haplotypes, namely haplotype 9 (17.1%) and haplotype 1 (56.1%). This frequency of mutant haplotype 1 in Portugal is, to our knowledge, the highest for this mutant haplotype in all studies reported to date. Other mutant haplotypes were either rare (haplotype 2, 9.7%) or totally absent (haplotype 3, 0%). Only 24.5% of all mutant alleles were found to consistently carry identified mutations, particularly R261Q (9.8%), R252W (3.3%), R408W (1.6%) and I94 (3.3%). A new mutation, L249F, located in the seventh exon of the gene, accounted for 6.5% of all mutant alleles in our series. Interestingly, this mutant genotype was consistently associated with mutant haplotype 1 (P<0.01), as also observed for the R261Q mutation. It appears, therefore, that mutant haplotype 1 is genotypically heterogeneous in Portugal and that more than two mutations account for its prevalence in this country.     

Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation

Heterogeneity of DNA methylation status among alleles is observed in various cell types and is involved in epigenetic gene regulation and cancer biology. However, the individual methylation profile within each allele has not yet been examined at the whole-genome level. In the present study, we applied linkage disequilibrium analysis to the DNA methylation data obtained from whole-genome bisulfite sequencing studies in mouse germline and other types of cells. We found that the methylation status of 2 consecutive CpG sites showed deviation from equilibrium frequency toward concordant linkage (both methylated or both unmethylated) in germline cells. In the imprinting loci where methylation of constituent alleles is known, our analysis detected the deviation toward the concordant linkage as expected. In addition, we applied this analysis to the transitional zone between methylated and unmethylated regions and to the cells undergoing epigenetic reprogramming. In both cases, deviation to the concordant-linked alleles was conspicuous, indicating that the methylation pattern is not random but rather concordant within each allele. These results will provide the key to understanding the mechanism underlying allelic heterogeneity.     

Linkage disequilibrium in Bougainville Island

Linkage disequilibria are estimated for three 2-locus systems in 18 samples from Bougainville Island, Solomon Islands. The systems are haptoglobin, acid phosphatase and MN blood group. The disequilibria are estimated two ways: by maximum likelihood (ML) and by the covariance between the non-alleles. Though seven of the 52 ML estimates are statistically different than zero, none of the covariance estimates are significant. We conclude that because linkage disequilibrium for loosely linked loci is a small quantity and because the sample sizes for most populations studied by anthropologists are small, linkage disequilibrium will not be a useful parameter for the study of natural selection in these populations.     

Linkage disequilibrium and gametophytic self-incompatibility

Summary The approach to linkage equilibrium of a locus linked to the locus determining gametophytic self-incompatibility (S) is considered. For the simplest case of three alleles at the S locus and two at the linked locus it is necessary to consider 3 measures of linkage disequilibrium. These are found to approach their equilibrium value of zero in one of three ways: 1) steadily declining to zero; 2) oscillating as decline proceeds; 3) a combination: 2) followed by 1). Linkage equilibrium may be established before genotype frequencies reach their expectation under random crossing. Earlier studies (Li 1951; Moran 1962) of the approach to S allele equilibrium have been based on the assumption that all types of pollen take part in fertilizations equally frequently. Such an assumption leads to simpler expressions for changes in S gene frequencies but is extremely unrealistic and, in particular, leads to a different rate of approach to equilibrium from the more comprehensive model. It is shown that even in the absence of selection it is not possible to predict the equilibrium gene frequency of a linked locus until S allele equilibrium is reached. This frequency may be either higher or lower than that calculated from a gene count in the starting genotype pool. However, these two gene frequencies may stabilize long before linkage equilibrium is achieved. An examination of selection against one genotype at the linked locus is undertaken. If linkage is complete, lethality can be less effective at reducing the gene frequency than is less intense selection (in only a few generations of selection). Here too linkage equilibrium may be established with selection still effective in bringing about a decline in gene frequency. An examination of the analysis and conclusions of Rasmuson (1980) shows that because these were based on the inadequate formulae previously discussed and exclude phenomena discussed above, they are misleading. The possibility of a gametophytic self-incompatibility system providing a sufficient condition for the sheltering of lethals in the absence of the condition of complete linkage to the S locus (r=0) is shown to be unlikely.     

Linkage disequilibrium at the Angelman syndrome gene UBE3A in autism families.

Autistic disorder is a neurodevelopmental disorder with a complex genetic etiology. Observations of maternal duplications affecting chromosome 15q11-q13 in patients with autism and evidence for linkage and linkage disequilibrium to markers in this region in chromosomally normal autism families indicate the existence of a susceptibility locus. We have screened the families of the Collaborative Linkage Study of Autism for several markers spanning a candidate region covering approximately 2 Mb and including the Angelman syndrome gene (UBE3A) and a cluster of gamma-aminobutyric acid (GABA(A)) receptor subunit genes (GABRB3, GABRA5, and GABRG3). We found significant evidence for linkage disequilibrium at marker D15S122, located at the 5' end of UBE3A. This is the first report, to our knowledge, of linkage disequilibrium at UBE3A in autism families. Characterization of null alleles detected at D15S822 in the course of genetic studies of this region showed a small (approximately 5-kb) genomic deletion, which was present at somewhat higher frequencies in autism families than in controls.     

植物基因组中的连锁不平衡

在植物基因组学研究领域, 连锁不平衡(linkage disequilibrium, LD)分析是近年来的一个研究亮点和热点。基于LD的作图方法不仅是新基因发掘的有效途径, 而且也是联系结构基因组学和表型组学的一座桥梁。自2001年基于LD的作图方法在植物中的成功运用至今, 已有大量关于植物基因组中LD结构及LD作图的研究报道。文章系统介绍了LD的基本理论及其在LD作图、单倍型多样性分析、单倍型标签SNP的开发和群体遗传学等研究中的应用, 并就近年来关于LD与群体结构、基因转换和上位效应及G×E互作等方面的研究热点和发展趋势进行了探讨。当前, 世界各国基因争夺大战日趋激烈。中国是基因资源大国, 但还不是基因大国。植物基因组中LD研究热潮的兴起及LD研究的进一步深入, 必将大大推动植物基因组学的快速发展, 特别是加速从作物种质资源中发掘新基因的进程。