Linkage of interleukin 6 locus to human osteopenia by sibling pair analysis

Osteopenia and osteoporosis are common human conditions considered to result from the interplay of multiple genetic and environmental factors. Twin and family studies have yielded strong correlations between levels of bone mass and a number of genetic factors. The genes involved could regulate metabolism, formation and resorption of bone, all processes that determine bone mass. We tested 192 sibling pairs of adult Japanese women from 136 families for genetic linkage between osteopenia and allelic variants of four candidate genes (interleukin-6, interleukin-6 receptor, calcium-sensing receptor, and matrix gla protein) using qualitative and quantitative methods, and using as genetic markers dinucleotide-repeat polymorphisms present in or near each of those loci. The interleukin-6 locus showed evidence of linkage to osteopenia analyzed as a qualitative trait, with mean allele sharing of 0.40 (P=0.0001) in discordant pairs and 0.55 (P=0.04) in concordant affected pairs. Variation at this locus was also linked to decreased bone mineral density measured as a quantitative trait (P=0.02). Analyses limited only to the post-menopausal women showed similar or even stronger results. No other locus among those tested showed any evidence of linkage by either method. The results provided strong evidence that genetic variation at the interleukin-6 locus affects regulation of bone mineral metabolism and confers risk for osteopenia and osteoporosis in adult women.     

Genetic polymorphism of adenosine deaminase and mannose phosphate isomerase in blood of arctic foxes, Alopex lagopus

Blood samples of 70 foxes, including 10 families, have been investigated by horizontal starch gel electrophoresis for the enzymes adenosine deaminase (ADA) and mannose phosphate isomerase (MPI). The observed variation of the enzymes could be explained as a result of one locus with two codominant alleles and one with three respectively. The segregation in the families of the alleles assumed for the two loci is in accordance with this genetic model. The frequency of the two alleles at the Ada locus is about the same and the slowest anodic migrating allele at the Mpi locus is the most frequent.     

Phenotypic assortative mating among the Peruvian Cashinahua

The persistence of behaviorally deleterious genes in the human population poses an interesting question for population genetics: If certain alleles at these loci are deleterious, why have they survived in the population? We consider evidence for phenotypic capacitance and/or frequency-dependent selection for an allele that has been putatively shown to have negative associations with human behaviors (the “short” 5-HTT promoter region allele) yet has persisted in human and nonhuman primate populations. Using data from the National Longitudinal Study of Adolescent Health, we compare sibling and twin variation in depression by 5-HTT genotype (specified in several ways) and investigate sibship-level cross-person gene-gene interactions. In support of the “orchid/dandelion” hypothesis, we find evidence that the short allele increases variation in phenotypes in response to environmental (or genetic) differences (i.e., acts as a perturbation of a phenotypic capacitor). Further, we also find some evidence that the effects of allelic variation at this locus are moderated by the genetic environment of the sibship unit (i.e., effects may be susceptible to frequency-dependent selection). We discuss implications of these findings for genetic models in general, specifically with respect to stable unit treatment value assumption violations (i.e., nonindependence of units of analysis).     

Multifactorial genetic models for quantitative traits in humans.

Quantitative traits measured in human families can be analyzed to partition the total population variance into genetic and environmental components, or to elucidate the genetic mechanism involved. We review the estimation of variance components directly from human pedigree data, or in the form of path coefficients from correlations between pairs of relatives. To elucidate genetic mechanisms, a mixed model that allows for segregation at a major locus, a polygenic effect and a sibling environmental correlation is described for nuclear families. In each case appropriate likelihoods are derived as a basis, using numerical maximum likelihood methods, for parameter estimation and hypothesis testing. A general model is then described that allows for several familial sources of environmental variation, assortative mating, and both major gene and polygenic effects; and an algorithm for calculating the likelihood of a pedigree under this model is indicated. Finally, some of the remaining problems in this area of biometric analysis are pointed out.     

蝗总科部分种类等位基因酶的比较研究

用水平淀粉凝胶电泳技术对采自山西太原黄陵、山西临猗伍姓湖及山西雁门关两科4种蝗虫的4个等位基因酶位点的基因频率进行了比较研究,并用BIOSYS-Ⅱ软件进行结果分析。结果表明：所研究种群的苹果酸脱氢酶（MDH）都存在两个位点,中华稻蝗的MDH-1还存在两条亚带。在所研究种群中的MDH-1图谱中,一个中等迁移率的谱带存在于所研究的4个种群中。东亚飞蝗在乳酸脱氢酶（LDH）和苹果酸酶（ME）中存在两个固定的等位基因,同时黄胫小车蝗在MDH-1中存在一个固定的等位基因,在MDH-2中存在一个独特的等位基因。在所有4个种群中,中华稻蝗遗传多样性水平最高（每个位点的等位基因数为3个,He=0.220）,黄胫小车蝗遗传多样性水平最低（每个位点的等位基因数为1.5个,He=0.013）。除中华稻蝗的MDH-1和LDH处于哈代-温伯格平衡,其余种群的4个位点的等位基因频率均不同程度的偏离哈代-温伯格平衡。等位酶数据表明这4个种群在系统发育关系方面是相近的,但在遗传多样性水平上却不同。     

The coalescent process in models with selection, recombination and geographic subdivision

A population genetic model with a single locus at which balancing selection acts and many linked loci at which neutral mutations can occur is analysed using the coalescent approach. The model incorporates geographic subdivision with migration, as well as mutation, recombination, and genetic drift of neutral variation. It is found that geographic subdivision can affect genetic variation even with high rates of migration, providing that selection is strong enough to maintain different allele frequencies at the selected locus. Published sequence data from the alcohol dehydrogenase locus of Drosophila melanogaster are found to fit the proposed model slightly better than a similar model without subdivision.     

A CA-repeat polymorphism close to the adenomatous polyposis coli (APC) gene offers improved diagnostic testing for familial APC.

Presymptomatic genetic testing for the presence of a mutant allele causing familial adenomatous polyposis coli (APC) has been difficult to perform effectively in the past because DNA markers surrounding the APC gene on chromosome 5q have not been very informative. We report results of genetic linkage studies on both research families and clinical families by using D5S346, a highly polymorphic dinucleotide (CA)-repeat locus 30-70 kb from the APC gene. Linkage analysis with this marker in a large APC pedigree showed an increase of at least 9.0 LOD units, in likelihood of linkage of the disease-causing allele to the APC locus, when compared with the highest LOD score attained with any other closely linked marker. When the first 14 APC families that requested genotypic analysis by the DNA Diagnostic Laboratory at the University of Utah were tested with D5S346, 20 of the 31 at-risk individuals were identified as either carriers or noncarriers of an APC-predisposing allele. We see this marker as an important tool for research studies and for the presymptomatic diagnosis of APC.     

Unequivocal determination of sire allele origin for multiallelic microsatellites when only the sire and progeny are genotyped

The effect of a segregating economic trait locus (ETL) can be detected with the aid of a linked genetic marker, if specific alleles of each locus are in association among the individuals genotyped for the genetic marker. For dairy cattle this can be achieved by application of the ‘granddaughter design’. If only the sires and their sons are genotyped for the genetic markers, then the allele origin of sons having the same genotypes as their sires cannot be determined. Seven sires and 101 sons were genotyped for five microsatellites. The mean frequency of heterozygous sires was 77%. The mean number of alleles per locus was 8.2. Frequency of informative sons per locus ranged from 60% to 80% with a mean of 72%. With highly polymorphic microsatellites, at least 60% more grandsire families can be included in the analysis, and the number of sons assayed can be reduced by 40%, as compared to diallelic markers.     

Effects of insect herbivory on early plant succession: comparison of an English site and an American site

We examined the survival, size, and agonistic behaviour of faster and slower developing rainbow trout ( Salmo gairdneri ) in an artificial stream channel with a simulated redd. The analysis was performed at two levels: between three full-sib families genetically marked at a hexosaminidase locus, and within families segregating for a regulatory allele Pgml-t(b) that is associated with faster developmental rate. The families differed significantly in their hatching times but showed little variation in emergence times. Fishes with the Pgml-t(b) allele hatched and emerged significantly earlier than their full-sibs without the allele. Despite the mortality of at least 50% of emerged fishes in the selection experiment, there was no significant difference in survival between either the three families or fishes with different genotypes at the Pgml-t locus. However, fishes from the faster developing family and those with the Pgml-t(b) allele had significantly higher levels of agonistic behaviour and had a tendency to be larger than slower developing individuals.     

Mapping quantitative trait loci with DNA microsatellites in a commercial dairy cattle population

Individual loci affecting economically important traits can be located using genetic linkage between quantitative trait loci and genetic markers. In the ‘granddaughter’ experimental design, heterozygous grandsires and their sons are genotyped for the genetic marker, while the quantitative trait records of the granddaughters are used for statistical analysis. Ten DNA microsatellite markers were used to look for associations with quantitative trait loci affecting milk production traits in seven Israeli Holstein grandsire families. At least 60% more grandsires were heterozygous, and 40% fewer individuals were discarded because of unknown paternal allele origin, as compared with diallelic markers. The effects of paternal alleles for locus D21S4 on kg milk and protein were significant (P < 0.025). The allele substitution effects for sire 783 were 283 kg milk and 5.7 kg protein. For both traits, progeny of sire 783 that inherited allele ‘18’ had higher evaluations than progeny that inherited allele ‘21’. These results were verified by genotyping 151 of his daughters. Thus, the rate of genetic gain for protein production can be increased by selecting progeny of sire 783 carrying allele ‘18’ at this locus.     

Mutation rate variation at human dinucleotide microsatellites

Mutation is the ultimate source of genetic variation, and mutation rate is thus an important parameter governing the extent of genetic variation. Microsatellites are highly informative genetic markers that have been widely used in genetic studies. While previous studies showed that the mutation rate differs in di-, tri-, and tetranucleotide repeats, how mutation rate distributes within each class of repeat is poorly understood. This study first revealed the pattern of the mutation rate variation within the dinucleotide repeats. Two data sets were used. The first is the allele frequency data from 115 microsatellites with dinucleotide repeats distributed along the human genome in 10 worldwide populations. The second data set is much larger, consisting of the allele frequency of 5252 dinucleotide repeats from the Genome Database. Mutation rate for each locus is estimated through a new homozygosity-based estimator, which has been shown to be unbiased and highly efficient and is reasonably robust against deviations from the single-step model. The mutation rates among loci can be approximated well by a gamma distribution and its shape parameter can be accurately estimated with this approach. This result provides the basic guidelines for analyzing the large-scale genomic data from microsatellite loci.     

Effects of environmental heterogeneity on victim-exploiter coevolution

We study victim-exploiter coevolution in a spatially heterogeneous island model. In each species, fitness consequences of between-species interactions are controlled by a single haploid diallelic locus. Our emphasis is on the conditions for the maintenance of genetic variation, the dynamic patterns observed, the extent of local adaptation and genetic differentiation between different demes, and on how different parameters (such as the strength and heterogeneity in selection, migration rates, and the number of sites) affect the dynamic and static behavior of the system. We show that under spatially homogeneous selection the maintenance of genetic variation is possible through asynchronous nonlinear dynamics where the allele frequencies in a majority of demes quickly synchronize but the rest do not. Spatially heterogeneous selection can maintain genetic variation even if migration rates are maximal. This happens in an oscillatory way. Genetic variation is most likely to be maintained at high levels if the heterogeneity in selection is large. If there are some restrictions on migration, genetic variation can be maintained at a stable equilibrium. This behavior is most likely at intermediate migration rates. In this case, the system can exhibit high spatial subdivision as measured by F(ST) values but relatively low local adaptation.     

Detection of genetic heterogeneity among pedigrees through complex segregation analysis: an application to hypercholesterolemia

Several methods for investigating genetic heterogeneity for extreme levels of a quantitative trait with hypothesized multiple genetic etiologies require a priori stratification of families and/or identification of distinct phenotypes among affected individuals. We present a statistical approach for detecting genetic heterogeneity that does not rely on either a priori stratification or discrete disease phenotypes. Complex segregation analysis was applied to total serum cholesterol measurements in 709 relatives of 98 healthy index cases selected from 3,666 school children surveyed for lipid levels in Rochester, Minnesota. Thirty-three of the index cases and 109 relatives had hypercholesterolemia (cholesterol levels greater than the 95th percentile for their age and sex). Through application of the mixed genetic model and then estimation of conditional probabilities for having the mutant allele at the major locus, genetic heterogeneity for hypercholesterolemia was indicated. In three of 70 pedigrees with one or more hypercholesterolemics, there is strong evidence for segregation at a major locus. In the remaining pedigrees, only polygene variation and/or environmental variation are associated with cholesterol variability. Grandparents in the three pedigrees that were segregating at the major locus had the highest rates of death due to coronary heart disease. This study establishes that the mixed model has the potential to identify pedigrees with different genetic etiologies for variability in quantitative traits.     

Sex‐specific recombination rates and allele frequencies affect the invasion of sexually antagonistic variation on autosomes

The introduction and persistence of novel, sexually antagonistic alleles can depend upon factors that differ between males and females. Understanding the conditions for invasion in a two‐locus model can elucidate these processes. For instance, selection can act differently upon the sexes, or sex linkage can facilitate the invasion of genetic variation with opposing fitness effects between the sexes. Two factors that deserve further attention are recombination rates and allele frequencies – both of which can vary substantially between the sexes. We find that sex‐specific recombination rates in a two‐locus diploid model can affect the invasion outcome of sexually antagonistic alleles and that the sex‐averaged recombination rate is not necessarily sufficient to predict invasion. We confirm that the range of permissible recombination rates is smaller in the sex benefitting from invasion and larger in the sex harmed by invasion. However, within the invasion space, male recombination rate can be greater than, equal to or less than female recombination rate in order for a male‐benefit, female‐detriment allele to invade (and similarly for a female‐benefit, male‐detriment allele). We further show that a novel, sexually antagonistic allele that is also associated with a lowered recombination rate can invade more easily when present in the double heterozygote genotype. Finally, we find that sexual dimorphism in resident allele frequencies can impact the invasion of new sexually antagonistic alleles at a second locus. Our results suggest that accounting for sex‐specific recombination rates and allele frequencies can determine the difference between invasion and non‐invasion of novel, sexually antagonistic alleles in a two‐locus model.     

D1S80 single-locus discrimination among African populations

The highly polymorphic D1S80 locus has no known genetic function. However, this variable number of tandem repeats (VNTR) locus has been highly valuable in forensic identification. In this study we report the allele and genotype frequencies of five African populations (Benin, Cameroon, Egypt, Kenya, and Rwanda), which can be used as databases to help characterize populations and identify individuals. The allele frequencies were used to infer genetic associations through phylogenetic, principal component, and G test statistical analyses. Compliance with Hardy-Weinberg equilibrium expectations was determined as were F(ST) estimates, theta p values, and power of discrimination assessment for each population. Our analyses of 28 additional populations demonstrate that the D1S80 locus alone can be used to discriminate geographic and ethnic groups. We have generated databases useful for human identification and phylogenetic studies.     

The effect of epistasis on sexually antagonistic genetic variation

There is increasing evidence of segregating sexually antagonistic (SA) genetic variation for fitness in laboratory and wild populations, yet the conditions for the maintenance of such variation can be restrictive. Epistatic interactions between genes can contribute to the maintenance of genetic variance in fitness and we suggest that epistasis between SA genes should be pervasive. Here, we explore its effect on SA genetic variation in fitness using a two locus model with negative epistasis. Our results demonstrate that epistasis often increases the parameter space showing polymorphism for SA loci. This is because selection in one locus is affected by allele frequencies at the other, which can act to balance net selection in males and females. Increased linkage between SA loci had more marginal effects. We also show that under some conditions, large portions of the parameter space evolve to a state where male benefit alleles are fixed at one locus and female benefit alleles at the other. This novel effect of epistasis on SA loci, which we term the ‘equity effect’, may have important effects on population differentiation and may contribute to speciation. More generally, these results support the suggestion that epistasis contributes to population divergence.     

A combined segregation and linkage analysis of insulin-dependent diabetes mellitus.

In an effort to clarify the mode of inheritance of insulin-dependent diabetes mellitus (IDDM), a total of 230 nuclear families with pointers were analyzed using the computer program COMBIN. Each family was ascertained without deliberate selection for multiplex families, and most families were completely typed for HLA-B, HLA-DR, and properdin factor B (Bf). There were 186 families with normal parents, 44 families with one affected parent, and no families with two affected parents. The computer program COMBIN evaluates evidence for a major locus of disease susceptibility, linkage of the major locus to a known genetic marker locus, linkage disequilibrium between the marker haplotypes and disease susceptibility, pleiotropic effects, and presence of an unlinked modifier. The parameters of COMBIN are T, Q, and D, representing the displacement, gene frequency of the IDDM allele, and dominance, respectively, of the major locus--and TM, QM, and DM being the analogous parameters of the modifier. In addition, the recombination fraction, theta, between the IDDM locus and HLA as well as the coupling frequencies are estimated. Finally, COMBIN simultaneously performs segregation and linkage analysis, with the optimal model being adjusted by the fit to the haplotype sharing distribution of IDDM. The results of these analyses indicated that the best-fitting genetic model of diabetic susceptibility appears to be a single major locus with near recessivity on a scale of standardized genetic liability, with gene frequency of the IDDM susceptibility allele of approximately 14%. In addition, the recombination fraction between the major locus and HLA is zero in all models; that is, for the B-BF-DR haplotype, the IDDM locus is tightly linked, probably (according to data from previous studies) to HLA-DR. Information determined by magnitude of coupling frequencies indicated that there is significant positive linkage disequilibrium with the haplotypes B8-BfS-DR4 and B15-BfS-DR4, significant negative linkage disequilibrium with B7-BfS-DR2, and intermediate disequilibrium for B8-BfS-DR3, B18-BfF1-DR3, and B40-BfS-DR4. Significant evidence in favor of an unlinked (to HLA) modifier (either single major locus or polygenes) could not be demonstrated. In conclusion, genetic susceptibility to IDDM appears to be most consistent with a single major locus with near recessivity that is tightly linked to HLA.     

The case for selection at CCR5-Delta32

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Delta32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Delta32 arose within the past 1,000 y and rose to its present high frequency (5%-14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit of much denser genetic maps and extensive control data. We find that the pattern of genetic variation at CCR5-Delta32 does not stand out as exceptional relative to other loci across the genome. Moreover using newer genetic maps, we estimated that the CCR5-Delta32 allele is likely to have arisen more than 5,000 y ago. While such results can not rule out the possibility that some selection may have occurred at C-C chemokine receptor 5 (CCR5), they imply that the pattern of genetic variation seen at CCR5-Delta32 is consistent with neutral evolution. More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome.     

Heterogeneity in IBD allele sharing among covariate-defined subgroups: issues and findings for affected relatives

OBJECTIVES: Modelling of variation in identical-by-descent (IBD) allele sharing using covariates can increase power to detect linkage, identify covariate-defined subgroups linked to particular marker regions, and improve the design of subsequent studies to localize genes and characterize their effects. In this report, we highlight issues that arise in studies of families with affected relatives. METHODS: Mirea et al. [Genet Epidemiol 2003, in press] extended linear and exponential linkage likelihood models [Kong and Cox, Am J Hum Genet 1997;61: 1179-1188] to model variation in NPL scores among covariate-defined groups of families, and proposed likelihood ratio (LR) and t statistics to detect differences in allele sharing between groups defined by a binary covariate. Here we evaluate factors affecting the power of these tests analytically and by example, as well as effects of constraints, nuisance parameters, and incomplete data on test validity by simulation of locus heterogeneity in families with affected siblings or affected cousins. RESULTS: Provided constraints on the parameters are avoided, these tests are particularly useful when one subgroup has less than expected IBD sharing. The distribution of the LR statistic depends on the extent of linkage, particularly in the presence of constraints. The t statistic may be biased by group differences in information content. CONCLUSIONS: We recommend that constraints be applied cautiously, and covariate effects in IBD allele sharing models interpreted with care.     

Estimation of Allele Frequencies at Isoloci

In some polyploid animals and plants, pairs of duplicated loci occur that share alleles encoding proteins with identical electrophoretic mobilities. Except in cases where these ``isoloci' are known to be inherited tetrasomically, individual genotypes cannot be determined unambiguously, and there is no direct way to assign observed variation to a particular locus of the pair. For a pair of diallelic isoloci, nine genotypes are possible but only five phenotypes can be identified, corresponding to individuals with 0-4 doses of the variant allele. A maximum likelihood (ML) approach is used here to identify the set of allele frequencies (p, q) at the individual gene loci with the highest probability of producing the observed phenotypic distribution. A likelihood ratio test is used to generate the asymmetrical confidence intervals around ML estimates. Simulations indicate that the standard error of p is typically about twice the binomial sampling error associated with single locus allele frequency estimates. ML estimates can be used in standard indices of genetic diversity and differentiation and in goodness-of-fit tests of genetic hypotheses. The noncentral χ(2) distribution is used to evaluate the power of a test of apparent heterozygote deficiency that results from attributing all variation to one locus when both loci are polymorphic.