HLA and disease: predictions for HLA haplotype sharing in families.

An analysis of published data on the segregation of HLA haplotypes in families with more than one individual affected with insulin-dependent diabetes mellitus or multiple sclerosis yields three conclusions: (1) In families with unaffected parents, affected sib pairs are much more often HLA haplotype identical in sibships with two affected sibs than in sibships with three or four affected sibs (P less than .01). (2) In families with unaffected parents and HLA half-identical affected sibs, well siblings more often receive the single haplotype not found in the affected sibs than is expected by chance (P less than .05). (3) In families with one affected parent, well siblings of affected individuals may share with the affected child a haplotype from the unaffected parent less than 50% of the time (P less than .10). These results are consistent with the premise that in some non-Mendelian, familial, HLA-associated disease more than one gene may contribute to susceptibility to the disorder.     

Empirical risk of oligophrenia in siblings of proband-oligophrenics in populations with high levels of inbreeding]

An investigation is carried out on 214 patients with oligophreny with regard to the secondary risk of the same disease for their four sibs. All patients were divided into 4 groups according to etiological symptoms, and it was found that maximal risk of the secondary disease with oligophreny was for the sibs of probably genetic group, and minimal one--for the sibs of the exogenic group. Maximal resemblance in the degree of the defect in the pair of proband-sibs was found both in probably-genetic and presumably-genetic groups. The risk of secondary oligophreny was significantly higher in sibs-probands with relatively lower degree of weak-mindedness than in those with severe mental defects. The frequency of the secondary oligophreny amond sibs of the inbred origin (18.9%) was more than twice as high (P less than 0.001) as in those of outbred origin (8.3%).     

Effect of individual and group rearing on age and size at maturity of male mosquitofish, Gambusia affinis

Age and size at sexual maturity were significantly greater for male mosquitofish, Gambusia affinis Baird and Girard, reared in sib-groups than for their sibs reared individually. Age at sexual maturity averaged 43.3 and 62.1 days for individually- and group-reared males, respectively, a 43% difference; final length and weight at maturity were 7.7 and 34.2% greater, respectively, for group-reared males than for their individually-reared sibs. The results were consistent among 30 families that represented the progeny of 30 wild-caught females. The observed differences may be attributable to behavioural interactions affecting the neuroendocrine control of the maturation process, as suggested by previous studies of Xiphophorus .     

A study of fluctuating dermatoglyphic asymmetry in the sibs and parents of cleft lip propositi.

Fluctuating asymmetry was studied in cleft lip propositi and their normal sibs and parents. The traits examined were a-b ridge counts and fingerprint patterns. Propositi with a family history of this congenital malformation and their normal sibs and parents were significantly different from the controls for this type of asymmetry. Propositi without a family history and their normal sibs and parents were similar to the controls. These results support the hypothesis that familial and sporadic cases of congenital cleft lip are different entities and give evidence for a genetic mechanism in the parents and sibs of the familial cases that may account for this congenital disorder and, concomitantly, increased fluctuating asymmetry.     

Red blood cell sorbitol dehydrogenase deficiency in a family with cataracts

Summary Sorbitol dehydrogenase (SORD) was quantitatively assayed in a family in which four out of five brothers and their father had bilateral cataracts. Three sibs (two of them with cataracts) and both their father and paternal grandfather had SORD activity of about 25% of the reference values; of the other two affected sibs one had about 50% and the other had 75%; the mother and two paternal uncles had about 75%. These results do not define a clear cataract-SORD deficiency etiopathogenic relationship, nevertheless, they strongly suggest activity polymorphism in human red cell SORD, which would be highly relevant not only to the study of cataracts but of other major complications in diabetes.     

Use of parents, sibs, and unrelated controls for detection of associations between genetic markers and disease.

Detecting the association between genetic markers and complex diseases can be a critical first step toward identification of the genetic basis of disease. Misleading associations can be avoided by choosing as controls the parents of diseased cases, but the availability of parents often limits this design to early-onset disease. Alternatively, sib controls offer a valid design. A general multivariate score statistic is presented, to detect the association between a multiallelic genetic marker locus and affection status; this general approach is applicable to designs that use parents as controls, sibs as controls, or even unrelated controls whose genotypes do not fit Hardy-Weinberg proportions or that pool any combination of these different designs. The benefit of this multivariate score statistic is that it will tend to be the most powerful method when multiple marker alleles are associated with affection status. To plan these types of studies, we present methods to compute sample size and power, allowing for varying sibship sizes, ascertainment criteria, and genetic models of risk. The results indicate that sib controls have less power than parental controls and that the power of sib controls can be increased by increasing either the number of affected sibs per sibship or the number of unaffected control sibs. The sample-size results indicate that the use of sib controls to test for associations, by use of either a single-marker locus or a genomewide screen, will be feasible for markers that have a dominant effect and for common alleles having a recessive effect. The results presented will be useful for investigators planning studies using sibs as controls.     

Seed provisioning within holly fruits: test of the hierarchical model

Seed provisioning within holly Ilex aquifolium fruits was examined after a controlled pollination experiment to obtain full-sibs. The distribution of dry mass in stony endocarp and endosperm was determined according to the rank in the size hierarchy of the sibs within fruit. Resources were more equally distributed among sibs in the endocarps than in the endosperms, which might suggest sibling competition among endosperms and no evidences of competition in the tissue controlled by the maternal sporophyte. When the sibs are ranked by size, seed provisioning fit reasonably with the hierarchical model. Differences among consecutive sibs increased down the hierarchy, the second sib in the size hierarchy was less variable in resource acquisition than the others, and the disparity in the distribution of resources among sibs decreased with fruit size increases. These results seems to be in accordance with both kin selection model and hierarchical model, which indicates at the same time control of resource provisioning by the maternal plant and differences in vigour among sibs. This revised version was published online in August 2006 with corrections to the Cover Date.     

CORRELATED MATINGS IN THE PARTIAL SELFER MIMULUS GUTTATUS

In partially selfing populations, siblings may be correlated for both selling and paternity. A model of the mating system based upon sampling pairs of progeny from a maternal parent is described. The model separates the correlation of selfing from the correlation of outcrossed paternal alleles and is an approach to paternity analysis suited for larger populations with fewer marker loci. Its parameters determine the components of genetic covariance between sibs and provide information about the average number of fathers in a maternal sibship. Electrophoretic markers were used to obtain estimates of correlated matings for two Mimulus guttatus populations. In both populations, about 50% selfing was observed. For two sibs randomly selected from the same capsule, the correlations of selfing between these sibs were 17% and 12% in the two populations, and the correlations of paternity (the proportion of full-sibs among outcrossed sib-pairs) were 37% and 44%. Sibs from different capsules were not correlated for selfing, and the paternity correlation dropped to near 20% in both populations. However, estimates of correlated matings have high variance, lack statistical independence, and can be difficult to obtain. The use of marker loci with many alleles can alleviate these problems.     

HLA and autoimmunity in North Indian type I (insulin-dependent) diabetic multiplex families

The HLA haplotype segregation and autoantibody spectrum in 7 type I (insulin-dependent) diabetic multiplex families of North Indian origin were determined. Of the total of 17 diabetic sibs, 7 shared both haplotypes and 3 shared one haplotype with the proband. No HLA-non-identical sibs were observed. This distribution of haplotypes was non-random (P approximately equal to 0.005). The mode of inheritance was compatible with an autosomal recessive model, while a dominant model was unlikely. Pancreatic islet-cell antibodies were found in 23.5% of affected sibs, but in no healthy family member. A high incidence of other autoantibodies (parietal-cell and thyroglobulin/thyroid microsomal antibodies) was detected in both the diabetic patients (26.3%), and in healthy first-degree relatives (22.2%). These findings emphasize the role of HLA-linked genes and autoimmunity in the pathogenesis of type I diabetes in North India.     

ABO and Rh blood groups in relation to sex ratio, mean number and mortality of sibs.

Data are presented on the sex ratio, mean number and mortality of the sibs of 17,060 schoolchildren, and on the sex ratio and mean number of the sibs of 5,785 blood donors, in relation to the children's and donors' sex and ABO and Rh blood groups. The sex ratio is significantly higher for the sibs of AB + B than for those of A + O schoolboys, and for the sibs of Rh-negative than for those of Rh-positive male blood donors, but in both cases the mean number of sibs is exactly the same for the first-mentioned as for the second-mentioned category.     

Genetic and immunologic aspects of type 1 diabetes mellitus

Prediction of type 1 diabetes mellitus (IDDM) and its identification in preclinical period is one of the central problems in modern medicine. They are based comprehensive genetic, immunologic and metabolic evaluations. We observed four hundred seven first-degree relatives of patients with IDDM (240 families in which one of the children or one of the parents had IDDM) have been included in the study. The study of HLA-DQA1, HLA-DQB1 polymorphic alleles and DRB1 genes and their combinations. The genetic study included searching HLA loci (HLA-DQA1, HLA-DQB1 polymorphic alleles and DRB1 genes) loci. To evaluate the genetic risk two approaches we used: first--carrying predisposing HLA-DQ alleles and DRB1-genes and it's combination (mainly associated in Russian population was DRB1*04-DQB1*0302, DRB1*04-DQA1*0301, DQA1*0301-DQB1*0302, DQA1*0301-DQB1*0302 and four susceptible alleles in A- and B- chains (Asp 57-, Arg 52+)) and second--IBD (identity by descent), in Russian population HLA-identical for 2 haplotypes sibs had risk of development of IDDM of 18%, for 1 haplotype--3%, for 0 haplotype-0.9%. The antibodies (ICA, IAA) prevalence rate has not depended on availability of predisposing HLA-DQ alleles and DRB1-genes and haploidentity of normal sibs and sibs with IDDM. However, GADA prevalence rate in groups having high predisposed alleles has been noticed as significantly higher (28.6%) comparing with 7.7% in groups that had no predisposing alleles (p < 0.05). The comparison of antibodies prevalence rate to sibs HLA-identity has shown the significant increase or GADA prevalence rate in group of siblings identical for one haplotype comparing with non-identical sibs (27.3% and 0% respectively, p < 0.001).     

Schizophrenia: the systematic construction of genetic models.

Methods are described for the systematic construction of genetic models of schizophrenia with one, two, and four loci. All models are constrained to fit the following three parameters: (1) frequency of schizophrenia in the general population = 0.9%; (2) frequency of schizophrenia in the sibs of schizophrenics = 8%; and (3) frequency of "schizophrenic spectrum" in the sibs of schizophrenics = 15%. In addition, a fourth parameter, the frequency of the allele predisposing to schizophrenia, is freely variable. The problems of correcting for ascertainment bias, and of comparing and testing these genetic models, are discussed.     

Genetic determination of mental activity parameters in the families of schizophrenic patients

Psychological parameters of mental activity (30 in total) and their genetic determination were studied in 67 families of schizophrenia patients (67 patients, 107 parent, and 30 sibs). Abnormalities of most of the examined characteristics were found in both the patients and their healthy relatives. Parameters of attention shifting and emotionality exhibited the largest genetic component (25-75 and 17-98%, respectively) in all analyzed groups of relatives (probands-affected sibs, probands-healthy sibs, healthy parents-healthy children, affected parents-affected children). Significant impact of genetic factors was also found in parameters "steadiness of attention under conditions of continuous concentration," "mediated retention span" "productivity of arbitrary retention by reproduction data," "personal anxiety level," "reflection of unusual social groups," and "self-assessment." The relationships among the characteristics examined in the system of mental activity were established by means of cluster analysis. The results of this study can be used in medical genetic counseling for identifying persons at high risk for schizophrenia.     

Inclusion of unaffected sibs increases power in model-free linkage analysis of a behavioral trait

Study design strategies are of critical importance in the search for genes underlying complex diseases. Two important design choices in planning gene mapping studies are the analytic strategy to be used, which will have an impact on the type of data to be collected, and the choice of genetic markers. In the present paper, we used the simulated behavioral trait data provided in the Genetic Analysis Workshop 14 to: 1) investigate the usefulness of incorporating unaffected sibs in model-free linkage analysis and, 2) compare linkage results of genome scans using a 7-cM microsatellite map with a 3-cM single nucleotide polymorphisms map. To achieve these aims, we used the maximum-likelihood-binomial method with two different coding approaches. We defined the unaffected sibs as those totally free of phenotypes correlated to the disease. Without prior knowledge of the answers, we were able to correctly localize 2 out of 5 loci (LOD > 3) in a sample of 200 families that included the unaffected sibs but only one locus when based on an affected-only strategy, using either microsatellite or SNPs genome scan. LOD scores were considerably higher using the analytic strategy which incorporated the unaffected sibs. In conclusion, including unaffected sibs in model-free linkage analysis of complex binary traits is helpful, at least when complete parental data are available, whereas there are no striking advantages in using single nucleotide polymorphisms over microsatellite map at marker densities used in the current study.     

A genetic study of Hirschsprung disease

Hirschsprung disease, or congenital aganglionic megacolon, is commonly assumed to be a sex-modified multifactorial trait. To test this hypothesis, complex segregation analysis was performed on data on 487 probands and their families. Demographic information on probands and the recurrence risk to relatives of probands are presented. An increased sex ratio (3.9 male:female) and an elevated risk to sibs (4%), as compared with the population incidence (0.02%), are observed, with the sex ratio decreasing and the recurrence risk to sibs increasing as the aganglionosis becomes more extensive. Down syndrome was found at an increased frequency among affected individuals but not among their unaffected sibs, and the increase was not associated with maternal age. Complex segregation analysis was performed on these family data. The families were classified into separate categories by extent of aganglionosis. For cases with aganglionosis beyond the sigmoid colon, the mode of inheritance is compatible with a dominant gene with incomplete penetrance, while for cases with aganglionosis extending no farther than the sigmoid colon, the inheritance pattern is equally likely to be either multifactorial or due to a recessive gene with very low penetrance. A model of gene action with random effects during morphogenesis is compatible with our observations.     

Clinico-genetic analysis of congenital biliary atresia

Clinical and genetic analysis of 148 cases of biliary atresia identified in our patients and the literature data allowed to establish the genetic heterogeneity for these congenital malformations, determine the contribution of congenital syndromes to their origin and estimate empirical risk for probands sibs. Possible reasons for a high (9.8%) recurrent risk in sibs of the patients with intrahepatic biliary atresia are discussed. Special examination of probands and their parents to differentiate risk and evaluate the possibility of prenatal diagnosis is proposed. A supposedly "new" syndrome with autosomal recessive mode of inheritance associated with extrahepatic biliary atresia is reported.     

Nonpaternity in Linkage Studies of Extremely Discordant Sib Pairs

An approach commonly used to increase statistical power in linkage studies is the study of extremely discordant sibling pairs. This design is powerful under both additive and dominant-gene models and across a wide range of allele frequencies. A practical problem with the design is that extremely discordant pairs that are ostensibly full sibs may be half sibs. Although estimates vary, the population rates of such nonpaternity may be as high as 5%-10%. The proportion in discordant pairs may be much higher. The present article explores this potential inflation as a function of the resemblance of sib pairs and the criteria for discordance used for selection.     

Multi-stemmed trees of Nothofagus pumilio second-growth forest in Patagonia are formed by highly related individuals

Background and Aims Multi-stemmed trees (tree clusters) in Nothofagus pumilio, a dominant tree species in Patagonia, are very uncommon and are restricted to the edge of second-growth forests following human-provoked fires. No vegetative reproduction has been reported so far. The genetic structure of multi-stemmed trees of this species was investigated and it was hypothesized that genets within a cluster were more closely related than average in the population. Methods Fifteen clusters (composed of at least three purported stems) and 15 single trees were sampled at the edge of a second-growth forest and genotyped using two amplified fragment length polymorphism (AFLP) primer pairs. We obtained 119 polymorphic markers that allowed clonality to be determined, together with sibship structure and relatedness among samples. Key Results Clonality was detected in seven clusters but all clusters had at least two different genotypes. Full sibs were found exclusively within clusters and in all clusters. Within a cluster, stems that were not identified as full sibs were often half sibs. Relatedness values for the full sibs and half sibs were higher than the theoretical values of 0·5 and 0·25 but the relatedness between clusters was very low. Conclusions Tree clusters that are merged at the edge of the second-growth forest of N. pumilio are composed of stems of the same genotype and of other genotypes that are highly related (but not always). It is suggested that this peculiar genetic structure results from a combination of several causes, including selection for merging of related individuals.     

Identity-by-descent genomic selection using selective and sparse genotyping

Background

Genomic selection methods require dense and widespread genotyping data, posing a particular challenge if both sexes are subject to intense selection (e.g., aquaculture species). This study focuses on alternative low-cost genomic selection methods (IBD-GS) that use selective genotyping with sparse marker panels to estimate identity-by-descent relationships through linkage analysis. Our aim was to evaluate the potential of these methods in selection programs for continuous traits measured on sibs of selection candidates in a typical aquaculture breeding population.

Methods

Phenotypic and genomic data were generated by stochastic simulation, assuming low to moderate heritabilities (0.10 to 0.30) for a Gaussian trait measured on sibs of the selection candidates in a typical aquaculture breeding population that consisted of 100 families (100 training animals and 20 selection candidates per family). Low-density marker genotype data (~ 40 markers per Morgan) were used to trace genomic identity-by-descent relationships. Genotyping was restricted to selection candidates from 30 phenotypically top-ranking families and varying fractions of their phenotypically extreme training sibs. All phenotypes were included in the genetic analyses. Classical pedigree-based and IBD-GS models were compared based on realized genetic gain over one generation of selection.

Results

Genetic gain increased substantially (13 to 32%) with IBD-GS compared to classical selection and was greatest with higher heritability. Most of the extra gain from IBD-GS was obtained already by genotyping the 5% phenotypically most extreme sibs within the pre-selected families. Additional genotyping further increased genetic gains, but these were small when going from genotyping 20% of the extremes to all phenotyped sibs. The success of IBD-GS with sparse and selective genotyping can be explained by the fact that within-family haplotype blocks are accurately traced even with low-marker densities and that most of the within-family variance for normally distributed traits is captured by a small proportion of the phenotypically extreme sibs.

Conclusions

IBD-GS was substantially more effective than classical selection, even when based on very few markers and combined with selective genotyping of small fractions of the population. The study shows that low-cost GS programs can be successful by combining sparse and selective genotyping with pedigree and linkage information.     

The sex ratio in spina bifida

It is shown that the well known excess of females in spina bifida children is statistically significant when they are compared with (a) the general population and (b) their sibs.Although there is a small excess of males amongst the sibs this is not statistically significant when compared with the general population and when all the children in these families are considered they appear to have a sex ratio very similar to that general population. The sibs of the parents of spina bifida children show a statistically significant excess of females.These findings are discussed with particular reference to the genetics of spina bifida.