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Evidence for a locus regulating total serum IgE levels mapping to chromosome 5.

Genetics studies of total serum IgE levels were performed since high IgE levels correlate with clinical expression of allergy and asthma. Families ascertained through a parent with asthma were genotyped for markers on 5q where there are multiple candidate genes that may influence the control of IgE and inflammation. Evidence for linkage of the IgE phenotype to 5q was obtained by both sib-pair and lod score analysis with evidence for recessive inheritance of high IgE levels from segregation analysis. These findings represent a major step in mapping genes important in the regulation of allergic responses and the pathogenesis of asthma.

Adult↗

A genetic study of subacute and chronic spinal muscular atrophy in childhood. A nosological analysis of 124 index patients.

A genetic study of the subacute spinal muscular atrophies (SMA) of late infancy and early childhood has been undertaken. All such patients with chronic disease (with ages at onset up to 14 years, and excluding SMA Type I) known to 2 large Neurological Centres were reassessed clinically and genetically. There were 124 index patients (67 females and 57 males) and 17 secondary cases, which formed two consecutive unselected series. To investigate the genetic composition of this group, 4 nosological approaches were used; cluster analysis of clinical features of the disease, Haldane's sib-sib analysis on familial cases, interpretation of frequency distribution histograms, and a segregation analysis. A single autosomal recessive gene accounts for over 90% of cases, causes a clinical syndrome which manifests its first clinical signs before 5 years of age and in almost all cases before two years of age, but which is compatible with life into the third decade. Moderate intrafamilial discordance for some clinical features may be observed, but no genetic heterogeneity within this group was demonstrated. A small group of cases is caused by (a) new dominant mutation(s), or (b) is composed of phenocopies, or both. This relatively uncommon form may comprise the majority of late-presenting cases, and may account for all cases which manifest the first signs after 5 years of age. The spectrum of age-at-onset of this group cannot be determined at present, but the disease may be manifest before the age of two years; it is clinically indistinguishable from SMA caused by an autosomal recessive gene. The literature has been reviewed in the light of these findings. Empirical risks for use in genetic counselling are presented.

Child, Preschool↗

Ethanol-nicotine interactions in long-sleep and short-sleep mice.

The possibility that common genetic factors regulate initial sensitivities to ethanol and nicotine as well as the development of cross-tolerance between these agents was explored using the long-sleep (LS) and short-sleep (SS) mice. The LS mice proved to be more sensitive to an acute challenge with nicotine than were the SS mice. Segregation analysis (F1, F2, backcross) indicated that ethanol sensitivity and nicotine sensitivity segregate together. Acute pretreatment with nicotine did not significantly affect sensitivity to ethanol, but ethanol pretreatment altered nicotine responsiveness. The LS mice develop more tolerance to nicotine and ethanol than do the SS and they also develop more cross-tolerance. These genetically determined differences in initial sensitivities, and tolerance and cross-tolerance development are not readily explained by differences in brain nicotinic receptor numbers.

Animals↗

A two-locus model for non-syndromic congenital dysplasia of the hip (CDH).

Complex segregation analysis was conducted in a sample of 171 pedigrees collected through probands affected by non-syndromic dysplasia of the hip (CDH) treated in Ferrara's CDH Centre in the period 1991-6. The analysis favoured a two-locus model, in which the accepted segregation model at the major locus was compatible with recessive transmission, with a gene frequency of the deleterious allele of around 0.20. For the other locus, among the Mendelian hypotheses tested, the recessive model turned out to be the most parsimonious. When ultrasonographic level was examined as an indication of severity, a significant improvement in the fit of the model was observed, giving clear evidence that information on the severity of CDH is important for a better definition of the hereditary transmission model.

Child↗

Robustness of the unified model to shared environmental effects in the analysis of dichotomous traits.

Simulation studies were conducted to assess to what extent the conclusions of segregation analysis, performed under the unified model, can be affected by the presence of unmeasured environmental factors shared by family members. Dichotomous data were generated on six-member nuclear families under two variants of the mixed model, incorporating environmental effects shared by all family members. When the generating model includes a polygenic component and a shared environmental effect, there is false detection of a major gene, especially when the joint likelihood of parents' and offspring's phenotypes is computed. The proportion of false conclusions increases as the shared environmental effect increases. On the other hand, the presence of a shared environmental effect in addition to a major gene component does not alter the detection of the major gene nor the transmission probability estimates, which are close to the expected Mendelian values. The rejection of the Mendelian transmission hypothesis, as observed in familial analyses of affected disorders, might be the result of mechanisms other than those considered here, such as more complex sources of environmental resemblance or a possible genetic heterogeneity.

Affective Disorders, Psychotic↗

Influence of apolipoprotein E genotype on the transmission of Alzheimer disease in a community-based sample.

The epsilon 4 allele of the apolipoprotein E locus (APOE) has been found to be an important predictor of Alzheimer disease (AD). However, linkage analysis has not clarified the role of APOE in the transmission of AD. The results of the current study provide evidence that the pattern of transmission of memory disorders differs in nuclear families in which the AD-affected proband did carry an epsilon 4 allele versus those families in which the AD-affected proband did not carry an epsilon allele. Further, risk of AD due to APOE genotype in the probands is modified by family history of memory disorders, suggesting gene-by-gene interactions. Family history remained a significant predictor of AD for affected probands with some, but not all, APOE genotypes in a logistic regression analysis. Though nonadditive in the prediction of AD, APOE genotype and family history acted additively in the prediction of age at AD onset. The results of complex segregation analysis were inconsistent with Mendelian segregation of memory disorders both in families of affected probands who did or did not carry an epsilon 4 allele, yet these two groups had significantly different parameter estimates for their transmission models. These results are consistent with gene-by-gene interactions, but also could result from common elements in the familial environment.

Age of Onset↗

Evidence for two unlinked loci regulating total serum IgE levels.

Studies investigating the genetic control of total serum IgE levels are of major importance in understanding basic pathophysiologic mechanisms in atopy and asthma, since IgE levels predict onset and correlate with the clinical expression of these disorders. Previous analysis of data from 92 families, ascertained through a parent with asthma, showed evidence for recessive inheritance of high IgE levels with linkage to chromosome 5q. Since there was significant residual familial correlation in the one-locus segregation analysis, two-locus segregation and linkage analyses were performed. Segregation analyses provided evidence for a second major locus unlinked to the locus on 5q. Utilization of this two-locus model corroborates the previous evidence for linkage between this trait and markers on 5q31-q33. The LODs for the most informative marker D5S436 increased from 3.00 at 10% recombination to 4.67 at 9% recombination, when the two-locus model was used. Additional linkage studies are needed to map this second locus. These results demonstrate the importance of performing multilocus segregation and linkage analyses for quantitative traits that are related to the phenotype of a complex disorder. This approach has given further insight into the genetics of allergy and asthma by providing evidence for a two-locus model.

Asthma↗

Pedigree analysis of plasmid segregation in yeast.

We have used pedigree analysis to investigate the mitotic segregation of circular and linear DNA plasmids in Saccharomyces cerevisae. Circular ARS plasmids, which bear putative chromosomal replication origins, have a high segregation frequency and a strong bias to segregate to the mother cell at mitosis. The segregation bias explains how the fraction of plasmid-bearing cells can be small despite the high average copy number of circular ARS plasmids. Linear ARS plasmids do not show strong segregation bias, nor does the 2 mu ori-containing plasmid YEp 13, when it is present in strains containing intact 2 mu circles. In the absence of endogenous 2 mu circles, YEp 13 behaves like an ARS plasmid, showing a strong maternal segregation bias. The presence of a centromere on circular ARS plasmids eliminates segregation bias. We discuss a model for plasmid segregation, which explains these findings and the possible biological significance of mother-daughter segregation bias.

DNA↗

Segregation and sporadic cases in families with Hunter's syndrome.

Segregation analysis on five samples of families with Hunter's syndrome (158 cases overall) shows that the mutant allele segregates in agreement with Mendelian expectations for an X linked recessive disease, but the proportion of sporadic cases is significantly lower than expected under mutation-selection equilibrium. Heterogeneity among the samples is apparent, but it is caused entirely by a sample of Ashkenazi families, whose segregation pattern has previously been interpreted as supporting the hypothesis of prenatal selection in favour of the pathological allele. Conversely, our joint analysis of the five samples by a maximum likelihood approach does not suggest segregation distortion. Possible reasons for the apparent lack of sporadic cases include the effect of ascertainment bias.

Alleles↗

CACTA and MITE transposon distributions on a genetic map of rice using F15 RILs derived from Milyang 23 and Gihobyeo hybrids.

Up to 35% of the rice genome consists of various kinds of transposons, and CACTA and MITE are two of the major class 2 DNA transposons in the genome. We have employed the consensus sequences of Rim2/Hipa CACTA, Stowaway MITE Pangrangja, and Tourist MITE Ditto for transposon display (TD) analysis to locate them on a genetic map, with 58 SSR markers used to anchor them. The TD analysis produced a high profile of the polymorphisms between the parental lines, Oryza sativa var. Gihobyeo/O. sativa var. Milyang, in intraspecific F15 RIL lines, locating 368 markers of Rim2/Hipa CACTA, 78 markers of Tourist MITE Ditto, and 22 markers of Stowaway MITE Pangrangja. In the segregation analysis, non-parental segregating bands and segregation distortion bands were observed. The recombinant genetic map spans 3023.9 cM, with 5.7 cM the average distance between markers. The TD markers were distributed unequally on the chromosomes because many TD markers were located in pericentric chromosomal regions except in the cases of chromosomes 2, 3, 6 and 9. Although the number of transposon markers was not sufficient to include all rice class 2 transposons, the current map of CACTA and MITE transposons should provide new insight into the genome organization of rice since no previous DNA transposon map is available.

Chromosome Mapping↗

Gene mapping and linkage analysis in Chinese hamster: assignment of the genes for APRT, LDHA, IDH2, and GAA to chromosome 3.

Interspecific somatic cell hybrids were generated by fusion of Chinese hamster spleen cells or primary fibroblasts with cells from an adenine phosphoribosyltransferase (APRT)-deficient mouse subline derived from LMTK- Cl.1D. Subclones which had been selected for either retention or loss of APRT were subjected to combined isozyme and chromosome segregation analysis. Concordant expression or segregation of Chinese hamster APRT, lactate dehydrogenase A (LDHA), isocitrate dehydrogenase 2 (IDH2), and alpha-glucosidase (GAA) with Chinese hamster chromosome 3 allowed provisional assignment of all four loci to that chromosome. Exceptional subclones, in which coordinate segregation of these syntenic markers was disrupted by chromosome breakage or deletions, allowed further localization of these genes to specific regions of the 3 chromosome.

Adenine Phosphoribosyltransferase↗

Evaluation of segregation ratio in Wilson's disease.

Two problems relating to segregation analysis for Wilson's disease are discussed and a practical solution is presented. A problem in the ascertainment of families with Wilson's disease is illustrated by comparing segregation ratios calculated by the single selection, complete truncate, and multiple incomplete selection methods. The effect on the segregation ratio of exclusion from the analysis of those sibs who had died of other diseases at a young age is also discussed and a method of adjustment of the number of the affected using the data on age at onset is proposed. The segregation ratio by multiple incomplete selection (Weinberg proband method) after adjustment for those sibs who had died of other diseases was 0.243, consistent with the theoretical value for autosomal recessive inheritance. The segregation ratio calculated by the single selection method tended to give a lower value, while that calculated by the complete truncate method was greater than the theoretical value. Recessive inheritance is, however, supported. The actual effect of exclusion of those sibs who had died of other diseases on gene frequency estimation is shown to be very small.

Gene Frequency↗

Asplenia syndrome in a child with a balanced reciprocal translocation of chromosomes 11 and 20 [46,XX,t(11;20)(q13.1;q13.13)].

We present a 6-year-old girl with a balanced 11;20 translocation [46,XX,t(11;20)(q13.1;q13.13)pat], asplenia, pulmonic stenosis, Hirschsprung disease, minor anomalies, and mental retardation. This case represents the second report of an individual with situs abnormalities and a balanced chromosome rearrangement involving a breakpoint at 11q13. Polymerase chain reaction (PCR) analysis of microsatellite markers excluded uniparental disomy for chromosomes 11 and 20. Segregation analysis of markers in the 11q13 region in the proposita and her phenotypically normal carrier sibs did not show a unique combination of maternal and paternal alleles in the patient. We discuss several possible explanations for the simultaneous occurrence of situs abnormalities and a balanced 11;20 translocation. These include (1) chance, (2) a further chromosome rearrangement in the patient, (3) gene disruption and random situs determination, and (4) gene disruption plus transmission of a recessive or imprinted allele from the mother.

Abnormalities, Multiple↗

MCMC segregation and linkage analysis.

Our objective was to infer the genetic model for the quantitative traits using a variety of methods developed in our group. Only a single data set was analyzed in any one analysis, although some comparison between data sets was made. In addition, the simulated model was not known during the course of the analysis. Basic modeling and segregation analyses for the five quantitative traits was followed by several simple genome scans to indicate areas of interest. A Markov chain Monte Carlo (MCMC) multipoint quantitative trait locus (QTL) mapping approach was then used to estimate the posterior probabilities of linkage of QTL to each chromosome simultaneously with trait model parameters, and to further localize the genes. Comparisons between the nuclear family and pedigree data sets indicated a greater power for QTL detection and mapping with the pedigree data sets. Even with the pedigree data, however, precise localization of the QTL did not appear to be possible using single replicate data sets. Two of the three genes with effects on trait Q1 were detected by the MCMC method.

Chromosome Mapping↗

Genetic and physical mapping of barley telomeres.

Barley (Hordeum vulgare L.) telomeres were investigated by means of pulsed field gel electrophoresis (PFGE) and in situ hybridization. In situ hybridization showed that a tandemly repeated satellite sequence has a subtelomeric location, and is present at thirteen of the fourteen chromosome ends. PFGE revealed that this satellite sequence is physically close to the telomeric repeat. Pulsed field gel electrophoresis was then used for segregation analysis and linkage mapping of several telomeric and satellite loci in a segregating doubled-haploid population. The telomeric repeat displayed a hypervariable segregation pattern with new alleles occurring in the progeny. Eight satellite and telomeric sites were mapped on an restriction fragment length polymorphism (RFLP)-map of barley, defining the ends of chromosome arms 1L, 2S, 3L, 4S, 4L, 5S and 6. One satellite locus mapped to an interstitial site on the long arm of chromosome 3. The physical location of this locus was confirmed by in situ hybridization to wheat/barley addition line 3.

Alleles↗

A new mouse cell-surface antigen (Ly-m20) controlled by a gene linked to Mls locus and defined by monoclonal antibodies.

Five monoclonal antibodies were established by the fusion of mouse myeloma cells (NS.1) with spleen cells from A and (A x C3H/An)F1 mice hyperimmunized with 70Z/3 tumor cells. These antibodies recognized a new antigenic specificity provisionally called Ly-m20.2. In direct cytotoxicity assays, 60 percent of cells in spleen, 40 percent in lymph node, 50 percent in bone marrow and less than 5 percent in thymus were found to react with three of the five antibodies, whereas the two others yielded somewhat lower cytotoxicity indices. The Ly-m20.2 antigen was also expressed on cells derived from liver and kidney but not on cells derived from brain. As judged from cytotoxicity assays with separated T and B cells, Ly-m20.2 antigen is carried preferentially on B lymphocytes. Direct plaque-forming cells (PFC) were completely eliminated by Ly-m20.2-specific antibody and complement. Linkage tests by analysis in 20 (CBA/J x C3H/An) x C3H/An backcross mice and by segregation analysis of BXH and SWXL recombinant inbred strains indicate close association of the loci controlling Ly-m20.2 and M1s antigens on chromosome 1.

Animals↗

GM1-gangliosidosis: chromosome 3 assignment of the beta-galactosidase-A gene (beta GALA).

The structural gene (beta GALA) coding for lysosomal beta-galactosidase-A (EC 3.2.1.23) has been assigned to human chromosome 3 using man--mouse somatic cell hybrids. Human beta-galactosidase-A was identified in cell hybrids with a species-specific antiserum to human liver beta-galactosidase-A. The antiserum precipitates beta-galactosidase-A from human tissues, cultured cells, and cell hybrids, and recognizes cross-reacting material from a patient with GM1 gangliosidosis. We have analyzed 90 primary man--mouse hybrids derived from 12 separate fusion experiments utilizing cells from 9 individuals. Enzyme segregation analysis excluded all chromosomes for beta GALA assignment except chromosome 3. Concordant segregation of chromosomes and enzymes in 16 cell hybrids demonstrated assignment of beta GALA to chromosome 3; all other chromosomes were excluded. The evidence suggests that GM1 gangliosidosis is a consequence of mutation at this beta GALA locus on chromosome 3.

Animals↗

An extremely polymorphic locus on the short arm of the human X chromosome with homology to the long arm of the Y chromosome.

A genomic DNA clone named CRI-S232 reveals an array of highly polymorphic restriction fragments on the X chromosome as well as a set of non-polymorphic fragments on the Y chromosome. Every individual has multiple bands, highly variable in length, in every restriction enzyme digest tested. One set of bands is found in all males, and co-segregates with the Y chromosome in families. These sequences have been regionally localized by deletion mapping to the long arm of the Y chromosome. Segregation analysis in families shows that all of the remaining fragments co-segregate as a single locus on the X chromosome, each haplotype consisting of three or more polymorphic fragments. This locus (designated DXS278) is linked to several markers on Xp, the closest being dic56 (DXS143) at a distance of 2 cM. Although it is outside the pseudoautosomal region, the S232 X chromosome locus shows linkage to pseudoautosomal markers in female meiosis. In determining the X chromosome S232 haplotypes of 138 offspring among 19 families, we observed three non-parental haplotypes. Two were recombinant haplotypes, consistent with a cross-over among the S232-hybridizing fragments in maternal meiosis. The third was a mutant haplotype arising on a paternal X chromosome. The locus identified by CRI-S232 may therefore be a recombination and mutation hotspot.

Cell Line↗