Simulation study comparing interval estimates for the recombination fraction

Three interval estimation procedures were evaluated to determine the method which provides the most accurate estimates for the recombination fraction, 0. The lod-0.83 support interval, the jackknife confidence interval, and the confidence interval based on estimated asymptotic standard error were compared by calculating the coverage probabilities of each. Family data that were simulated under the model of a single fully penetrant, dominant disease locus at some distance, 0, from fully informative matings were used. Comparisons were based on 1,000 random samples of size 20,60, and 100 families. In addition, a methodology for obtaining prediction intervals for 0 was developed. This procedure is of practical use and does not require asymptotic assumptions based on large sample theory. The results provide an a priori idea about precision of the estimates, as well as empirical interval estimates of 0. Graphs of the authors' Monte Carlo intervals are presented for these simulations. Investigators studying different traits, however, could condition specifically on the family structure and distribution of the disease they are investigating and obtain similar graphs.

Using lod-score differences to determine mode of inheritance: a simple, robust method even in the presence of heterogeneity and reduced penetrance

Determining the mode of inheritance is often difficult under the best of circumstances, but when segregation analysis is used, the problems of ambiguous ascertainment procedures, reduced penetrance, heterogeneity, and misdiagnosis make mode-of-inheritance determinations even more unreliable. The mode of inheritance can also be determined using a linkage-based method (maximized maximum lod score or mod score) and association-based methods, which can overcome many of these problems. In this work, we determined how much information is necessary to reliably determine the mode of inheritance from linkage data when heterogeneity and reduced penetrance are present in the data set. We generated data sets under both dominant and recessive inheritance with reduced penetrance and with varying fractions of linked and unlinked families. We then analyzed those data sets, assuming reduced penetrance, both dominant and recessive inheritance, and no heterogeneity. We investigated the reliability of two methods for determining the mode of inheritance from the linkage data. The first method examined the difference (delta) between the maximum lod scores calculated under the two mode-of-inheritance assumptions. We found that if delta was > 1.5, then the higher of the two maximum lod scores reflected the correct mode of inheritance with high reliability and that a delta of 2.5 appeared to practically guarantee a correct mode-of-inheritance inference. Furthermore, this reliability appeared to be virtually independent of alpha, the fraction of linked families in the data set, although the reliability decreased slightly as alpha fell below .50.(ABSTRACT TRUNCATED AT 250 WORDS)

Pre- and post-synaptic modulators of excitatory neurotransmission: comparative effects on hypoxia/hypoglycemia in cortical cultures

Neuron-enriched cultures from embryonic rat cerebral cortex were exposed to hypoxia and hypoglycemia, and the resulting cellular injury was quantified by measuring lactate dehydrogenase (LDH) release, which was maximal after 20-24 h. The increase in LDH release produced by hypoxia/hypoglycemia was prevented by N-methyl-D-aspartate (NMDA) antagonists, but not by three classes of drugs thought to modulate glutamate release: Ca2+ channel antagonists (nimodipine, omega-conotoxin GVIA, omega-agatoxin-IVA), KATP channel activators (cromakalim, diazoxide), and glutamate transport inhibitors (dihydrokainate, DL-threo-beta-hydroxyaspartate).

A comparison of multiplex and simplex families with Alzheimer's disease/senile dementia of Alzheimer type within a well defined population

A study was made on 150 clinically demented patients presenting at autopsy at Umeå University Hospital in Sweden. In 90 of the cases dementia was considered to be primary in nature and of these forty six per cent (41 cases), fulfilled both the clinical and histopathological criteria for the diagnosis of Alzheimer's disease/Senile dementia of Alzheimer type (AD/SDAT). The families of these 41 AD/SDAT cases were then studied, and a family history obtained through interviews with multiple family informants and from civil and medical records. Additional diseased family members suffering from progressive dementia (multiplex families) were observed in 12 probands out of 41 (29%). Multiplex families exhibited similar clinical and histopathological characteristics as simplex families containing a single affected individual. The secondary cases in the multiplex families exhibited similar demographic and clinical characteristics as the probands. 39% of the multiplex and 14% of the simplex cases had an early age of onset of the disease, that was under 65 years. The overall prevalence of progressive dementia disorders in the 41 families was 5.9%. The prevalence of a progressive dementia disorder was 11% in the multiplex families (14% for the early onset cases) and 3.5% in the simplex families (2% for the early onset cases). The prevalence of progressive dementia disorder for family members who had passed the mean age of the onset of the disease for their family, was 45% for multiplex and 18% for simplex families. Furthermore the incidence rate for dementia was significantly higher (p < 0.005) in multiplex families (5.5 per 1,000 person years) when compared to simplex families (2.5 per 1,000 person years). No differences could be seen in parental age at birth of the diseased when comparing the two sets of families. However in multiplex families the duration of the disease was significantly (p < 0.025) shorter, in subjects with parental age at birth over 35 years compared to those with a parental age under 35 years. The multiplex families contained significantly (p < 0.025) larger sibships; and showed a significantly lower age of onset for the disease (p < 0.001), and a significantly longer duration of disease (p < 0.05) compared to the simplex families. A significant intra familial correlation of age at disease onset was observed in both sets of the families.

Enhancement of NMDA toxicity and calcium responses by chronic exposure of cultured cortical neurons to ethanol

Exposure of rat cerebrocortical cultures to 100 mM ethanol for 3-4 days increased both the neurotoxic potency of N-methyl-D-aspartate (NMDA) and the maximal extent of NMDA-induced intracellular calcium (Ca2+i) elevations. In both control and ethanol-treated cultures, NMDA toxicity correlated closely with [Ca2+]i. Enhancement of NMDA responses may reflect neuronal adaptation to chronic ethanol exposure and could contribute to the pathogenesis of alcohol-related neurologic disorders.

Calcium indicators and excitotoxicity in cultured cortical neurons

Membrane-permeating, fluorescent Ca2+ indicators have been used to investigate the role of increased intracellular Ca2+ (Ca2+i) levels in excitotoxic neuronal injury, but their ability to chelate Ca2+i and their own toxic effects in some cells could obscure this relationship. N-Methyl-D-aspartate (NMDA)-stimulated Ca2+i responses and toxicity were measured in neuron-enriched rat cerebrocortical cultures loaded with either fluo-3 or fura-2. Ca2+i responses signaled by both indicators were similar in magnitude, and neither indicator reduced NMDA toxicity, measured by lactate dehydrogenase (LDH) release. Fluo-3 and fura-2 appear to be suitable for comparative studies of NMDA-induced Ca2+i responses and excitotoxicity.

Adequacy of single-locus approximations for linkage analyses of oligogenic traits: extension to multigenerational pedigree structures

When a disease is controlled by two or more mendelian loci acting epistatically, it can be modeled in a linkage analysis as a single-locus mendelian disease with reduced penetrance. Previous work has demonstrated the reliability of such approximation for nuclear families, but not for extended pedigrees. We simulated extended pedigrees under two-locus models, in which one of the two disease loci was linked to a marker, and analyzed them both under the correct two-locus models and under single-locus approximations. The single-locus approximations provided results that were very close to the correct two-locus results. This held true, whether we ascertained pedigrees based on the presence of at least one affected individual, or based on the presence of at least five affected individuals. While a simulation study cannot guarantee that extrapolation of the results to models other than those examined is justified, our findings strongly suggest that single-locus linkage analysis can be reliably used in analyzing two-locus disorders in extended pedigrees. We also found striking confirmation of the importance of performing linkage analyses under both dominant and recessive models when the mode of inheritance is unknown, for extended pedigrees ascertained through multiple affected individuals.

Ethanol and sedatives

Ethanol abuse is associated with a variety of neurologic disturbances. These disturbances result from direct drug effects, drug withdrawal, nutritional deficiency, organ system failure, and other, unidentified factors. In contrast, abuse of sedative-hypnotic drugs produces a more limited spectrum of neurologic involvement, consisting primarily of overdose and withdrawal syndromes. Recent advances in pathophysiology, diagnosis, and treatment are beginning to influence the clinical approach to some of these disorders.

The application of jackknife statistics to estimates of the recombination fraction

We develop and evaluate the jackknife statistics [Efron, 1982] for obtaining confidence intervals for the recombination fraction. We consider two cases: (1) a single sibship of size S with phase known parents (one doubly heterozygous and one doubly homozygous) and (2) a sample of 20 nuclear families. We compare the jackknife confidence interval to the -1.00 lod and -0.83 lod intervals. For the first case we compare our intervals with a confidence interval which we develop that has coverage of exactly 95%. For the second case, we do a simulation study and compare the coverage of the intervals and the endpoints of the intervals with the actual 2.5th and 97.5th percentiles. Our results indicate that in case (1) the lod intervals provide closer estimates to the 95% exact interval than does the jackknife approach. However, in case (2), although the lod intervals have better coverage probabilities, the jackknife interval endpoints are closer to the actual percentile points than either of the lod interval endpoints.

Linkage analysis of "necessary" disease loci versus "susceptibility" loci

The association of some diseases with specific alleles of certain genetic markers has been difficult to explain. Several explanations have been proposed for the phenomenon of association, e.g. the existence of multiple, interacting genes (epistasis) or a disease locus in linkage disequilibrium with the marker locus. One might suppose that when marker data from families with associated diseases are analyzed for linkage, the existence of the association would assure that linkage will be found, and found at a tight recombination fraction. In fact, however, linkage analyses of some diseases associated with HLA, as well as diseases associated with alleles at other loci located throughout the genome, show significant evidence against linkage, and others show loose linkage, to the puzzlement of many researchers. In part, the puzzlement arises because linkage analysis is ideal for looking for loci that are necessary, even if not sufficient, for disease expression but may be much less useful for finding loci that are neither necessary nor sufficient for disease expression (so-called susceptibility loci). This work explores what happens when one looks for linkage to susceptibility loci. A susceptibility locus in this case means that the allele increases risk but is neither necessary nor sufficient for disease expression. It might be either an allele at the marker locus itself that is increasing susceptibility or an allele at a locus in linkage disequilibrium with the marker. This work uses computer simulation to examine how linkage analyses behave when confronted with data from such a model.(ABSTRACT TRUNCATED AT 250 WORDS)

Lack of disease associated HLA-DQ restriction fragment length polymorphisms in families with autoimmune thyroid disease

Autoimmune thyroid disease (AITD) is often familial and serological HLA disease associations have been described in many different populations. However, such HLA disease associations are weak and the precise molecular contribution of HLA antigens to thyroid disease susceptibility remains unknown. Much of the data available are cross-sectional and few studies have explored familial inheritance of AITD at the molecular level. We have, therefore, examined the inheritance of AITD in multiplex and multi-generational families using restriction fragment length polymorphism (RFLP) analysis of DNA digested with the restriction enzyme BamH1 and probed with a full length human HLA-DQ beta cDNA probe. Thirty seven subjects in 7 informative families were available for study. Eleven subjects had Graves' disease and 4 were diagnosed as having Hashimoto's thyroiditis. Segregation of polymorphic fragments enabled genotyping of each individual to produce fully informative families. LOD scores were computed, using the LIPED program, for dominant and recessive models of inheritance, for recombination fractions of 0.01 to 0.5 for each sex, and for penetrances of 0.1 to 1.0. The results showed that maximum LOD scores were negative for all of the inheritance models tested. If the primary locus for AITD were in the HLA region, LOD scores would be highly positive. These data, therefore, provide strong evidence against a disease locus for AITD in linkage disequilibrium with the HLA-DQ beta locus.

Ethanol and excitotoxicity in cultured cortical neurons: differential sensitivity of N-methyl-D-aspartate and sodium nitroprusside toxicity

Neural injury due to ischemia and related insults is thought to involve the action of excitatory amino acids at N-methyl-D-aspartate receptors, which results in the influx of extracellular Ca2+ and the generation of nitric oxide. Because ethanol inhibits physiologic responses to excitatory amino acids, we examined its effect on toxicity induced by N-methyl-D-aspartate and by the nitric oxide donor sodium nitroprusside in neuron-enriched cultures prepared from rat cerebral cortex. Both N-methyl-D-aspartate and sodium nitroprusside were cytotoxic, as measured by the release of lactate dehydrogenase and by microfluorescent determination of cell viability. Ethanol (3-1,000 mM) protected cultures from N-methyl-D-aspartate but not sodium nitroprusside toxicity, and the ability of a series of n-alkanols to reproduce the effect of ethanol was related to carbon-chain length. Neuroprotection by ethanol was accompanied by a decrease in the N-methyl-D-aspartate-evoked elevation of free intracellular Ca2+ and did not appear to involve gamma-aminobutyric acid- or cyclic GMP-mediated mechanisms. These findings suggest that ethanol inhibits excitotoxicity at an early step in the N-methyl-D-aspartate signaling pathway, probably by reducing Ca2+ influx, and not by interfering with the action of nitric oxide.

Antiparkinsonian drugs and in vitro excitotoxicity

N-Methyl-D-aspartate (NMDA) receptor activation has been implicated in the pathogenesis and clinical expression of Parkinson's disease. Because some antiparkinsonian drugs have NMDA antagonist properties, we examined their effects on NMDA toxicity, measured by lactate dehydrogenase (LDH) release, in neuron-enriched cerebrocortical cultures. Amantadine reduced NMDA toxicity with half-maximal reduction at approximately 30 microM, while trihexphenidyl, L-3,4-dihydroxyphenylalanine (L-DOPA), bromocriptine and selegiline were ineffective, and benztropine was itself toxic. Amantadine and related drugs could not only reduce parkinsonian symptoms, but also modify underlying neurodegenerative processes.

Inter- and intrafamilial heterogeneity: effective sampling strategies and comparison of analysis methods

Heterogeneity, both inter- and intrafamilial, represents a serious problem in linkage studies of common complex diseases. In this study we simulated different scenarios with families who phenotypically have identical diseases but who genotypically have two different forms of the disease (both forms genetic). We examined the proportion of families displaying intrafamilial heterogeneity, as a function of mode of inheritance, gene frequency, penetrance, and sampling strategies. Furthermore, we compared two different ways of analyzing linkage in these data sets: a two-locus (2L) analysis versus a one-locus (SL) analysis combined with an admixture test. Data were simulated with tight linkage between one disease locus and a marker locus; the other disease locus was not linked to a marker. Our findings are as follows: (1) In contrast to what has been proposed elsewhere to minimize heterogeneity, sampling only "high-density" pedigrees will increase the proportion of families with intrafamilial heterogeneity, especially when the two forms are relatively close in frequency. (2) When one form is dominant and one is recessive, this sampling strategy will greatly decrease the proportions of families with a recessive form and may therefore make it more difficult to detect linkage to the recessive form. (3) An SL analysis combined with an admixture test achieves about the same lod scores and estimate of the recombination fraction as does a 2L analysis. Also, a 2L analysis of a sample of families with intrafamilial heterogeneity does not perform significantly better than an SL analysis. (4) Bilineal pedigrees have little effect on the mean maximum lod score and mean maximum recombination fraction, and therefore there is little danger that including these families will lead to a false exclusion of linkage.

There is more than one way to collect data for linkage analysis. What a study of epilepsy can tell us about linkage strategy for psychiatric disease

The most popular strategy for finding genes in psychiatric diseases has been to focus on large pedigrees with many affected members. While this strategy has sound advantages, it also has drawbacks that have seldom been addressed. The strategy of using smaller families also has its place in a linkage analysis. To illustrate the point, I discuss herein the successful search for a gene for another common complex disease, namely, idiopathic primary generalized epilepsy. There, investigators in the Los Angeles (Calif) Epilepsy Program used mostly nuclear families who were chosen through a proband with highly specific characteristics. An independent study, using a different strategy but one still focused on small families, then confirmed the linkage. However, investigators of both epilepsy projects put much care into determining which clinical characteristics would be used to define the index cases. The implications for the study of psychiatric disease are as follows: (1) careful attention must be paid to clinical presentation, and (2) there is room for both large-pedigree and small-family strategies in designing linkage studies.

Possible association of juvenile myoclonic epilepsy with HLA-DRw6

Juvenile myoclonic epilepsy (JME) is a clearly defined subform of idiopathic generalized epilepsy with a high aggregation of epilepsy in family members. With the HLA-system used as a genetic marker, a linkage between JME and the HLA region was demonstrated. Linkage with the HLA region suggests that JME may be associated with an HLA-antigen. An association could indicate that the gene lies in the HLA region and is in linkage disequilibrium with one of the HLA-antigens. Eighty-eight unrelated patients with JME were typed for the HLA-A and HLA-B locus, 77 were typed for the HLA-C locus, and 76 were typed for the DR locus. The antigen frequency was compared with those of healthy blood donors. The highest difference was noted in the frequency of DRw6 (39.5% in patients vs. 22.1% in controls). This weak association is open to question because DRw6 is known to split into DRw13 and DRw14.

A novel inhibitor of glutamate release reduces excitotoxic injury in vitro

Excessive release of glutamate has been implicated in the pathogenesis of excitotoxic neurologic disorders, such as stroke. BW 1003C87, an inhibitor of glutamate release and a putative Na+ channel antagonist, reduced veratridine-stimulated, tetrodotoxin- and dizocilpine-sensitive toxicity (measured by lactate dehydrogenase efflux) in neuron-enriched cortical cultures (IC50 = 5 microM). In contrast, BW 1003C87 (300 microM) had no effect on toxicity induced by direct application of 1 mM glutamate or 1 mM N-methyl-D-aspartate, or by depolarization with 50 mM KCl. Glutamate release inhibitors such as BW 1003C87 may provide a novel approach to protection from excitotoxicity.

Sensitivity of lod scores to changes in diagnostic status

This paper investigates effects on lod scores when one individual in a data set changes diagnostic or recombinant status. First we examine the situation in which a single offspring in a nuclear family changes status. The nuclear-family situation, in addition to being of interest in its own right, also has general theoretical importance, since nuclear families are "transparent"; that is, one can track genetic events more precisely in nuclear families than in complex pedigrees. We demonstrate that in nuclear families log10 [(1-theta)/theta] gives an upper limit on the impact that a single offspring's change in status can have on the lod score at that recombination fraction (theta). These limits hold for a fully penetrant dominant condition and fully informative marker, in either phase-known or phase-unknown matings. Moreover, log10 [(1-theta)/theta] (where theta denotes the value of theta at which Zmax occurs) gives an upper limit on the impact of a single offspring's status change on the maximum lod score (Zmax). In extended pedigrees, in contrast to nuclear families, no comparable limit can be set on the impact of a single individual on the lod score. Complex pedigrees are subject to both stabilizing and destabilizing influences, and these are described. Finally, we describe a "sensitivity analysis," in which, after all linkage analysis is completed, every informative individual in the data set is changed, one at a time, to see the effect which each separate change has on the lod scores. The procedure includes identifying "critical individuals," i.e., those who would have the greatest impact on the lod scores, should their diagnostic status in fact change. To illustrate use of the sensitivity analysis, we apply it to the large bipolar pedigree reported by Egeland et al. and Kelsoe et al. We show that the changes in lod scores observed there, on the order of 1.1-1.2 per person, are not unusual. We recommend that investigators include a sensitivity analysis as a standard part of reporting the results of a linkage analysis.