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Results for “crossover”

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PubMed2001

Comparison of the statistical efficiency of case-crossover and case-control designs: application to severe cutaneous adverse reactions.

Although case-crossover analyses have lately emerged as an alternative to case-control analyses in epidemiological studies, it is not yet known in which situations they give reliable conclusions. In this work, the case-crossover and the case-control designs were first compared on the basis of a dataset from a published study of severe cutaneous adverse reactions resulting from drug exposures of various durations and prevalences of use (245 cases, 1147 controls, and exposures to 23 drug classes). Next, the statistical efficiency of each design was compared via Monte Carlo simulations. Eight of the 13 risk factors identified by case-control analysis of the published data were also identified by the case-crossover analysis, with fairly good agreement on ranks of risk estimates (Spearman's correlation coefficient = 0.71, P < 0.001 ). Simulation studies showed that for relative risks below 8, the case-crossover design (250 cases, 4 control periods/case) had a higher power than the case-control design (250 cases, 4 controls/case), and that the case-crossover design was more conservative than the case-control design for prevalences of drug use below 10%. We conclude that the case-crossover design is not suitable for long-term exposures, but is an appropriate alternative for assessing rare risks associated with transient to short-term exposures.

Case-Control Studies↗

PubMed1997

Direct evidence for Holliday junction crossover isomerization.

The Holliday junction is a key intermediate in genetic recombination. This is a four-stranded branched DNA structure, whose double-helical arms are stacked in two domains; two of the strands are roughly helical, and the other two cross over between domains. Switching the strands between these two roles is known as crossover isomerization; this postulated reversal is thought to be one of the key transformations that the Holliday junction can undergo, because it can lead to changing the products from patch to splice recombinants. We present direct evidence that this reaction can indeed occur in Holliday junctions in solution. We have constructed a double-crossover molecule containing a branched junction, constrained not to be in its favored conformation. This junction is released from the double-crossover molecule by digestion with restriction endonucleases. We demonstrate by means of hydroxyl radical autofootprinting that the junction changes its crossover isomer spontaneously when released from the double crossover. We control for the possibility that the experimental protocol causes the isomerization. We also exclude dissociation and interaction with other molecules in solution as contributing to the phenomenon. Thus, crossover isomerization is an authentic spontaneous transformation of Holliday junctions.

Bacterial Proteins↗

PubMed2004

Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology.

Paranemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.

Circular Dichroism↗

PubMed2004

Crossover of marital dissatisfaction during military downsizing among Russian army officers and their spouses.

This study examined mechanisms of strain crossover within couples and the moderating role of gender. Data were collected at a time of military downsizing from a sample of 1,250 Russian army officers and their spouses. The authors tested a model that incorporated 3 mechanisms for the crossover of marital dissatisfaction among dual-earner couples. The model provided support for 2 suggested crossover mechanisms: direct reactions of crossover and indirect mediated effects through social undermining. Strong evidence was also provided for gender asymmetry in the crossover process. Marital dissatisfaction crossed over from husbands to wives but not vice versa, and social undermining behavior played a role in the process of crossover of marital dissatisfaction for husbands but not for wives.

Adult↗

PubMed2002

Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot.

Human DNA diversity arises ultimately from germline mutation that creates new haplotypes that can be reshuffled by meiotic recombination. Reciprocal crossover generates recombinant haplotypes but should not influence the frequencies of alleles in a population. We demonstrate crossover asymmetry at a recombination hot spot in the major histocompatibility complex, whereby reciprocal exchanges in sperm map to different locations in the hot spot. We identify a single-nucleotide polymorphism at the center of the hot spot and show that, when heterozygous, it seems sufficient to cause this asymmetry, apparently by influencing the efficiency of highly localized crossover initiation. As a consequence, crossovers in heterozygotes are accompanied by biased gene conversion, most likely occurring by gap repair, that can also affect nearby polymorphisms through repair of an extended gap. The result is substantial over-transmission of the recombination-suppressing allele and neighboring markers to crossover products. Computer simulations show that this meiotic drive, although weak at the population level, is sufficient to favor eventual fixation of the recombination-suppressing variant. These findings provide an explanation for the relatively uniform widths of human crossover hot spots and suggest that hot spots may be generally prone to extinction by meiotic drive.

Computer Simulation↗

PubMed2002

Crossover clustering and rapid decay of linkage disequilibrium in the Xp/Yp pseudoautosomal gene SHOX.

Crossover between the human sex chromosomes during male meiosis is restricted to the terminal pseudoautosomal pairing regions. An obligatory exchange occurs in PAR1, an Xp/Yp pseudoautosomal region of 2.6 Mb, which creates a male-specific recombination 'hot domain' with a recombination rate that is about 20 times higher than the genome average. Low-resolution analysis of PAR1 suggests that crossovers are distributed fairly randomly. By contrast, linkage disequilibrium (LD) and sperm crossover analyses indicate that crossovers in autosomal regions tend to cluster into 'hot spots' of 1-2 kb that lie between islands of disequilibrium of tens to hundreds of kilobases. To determine whether at high resolution this autosomal pattern also applies to PAR1, we have examined linkage disequilibrium over an interval of 43 kb around the gene SHOX. Here we show that in northern European populations, disequilibrium decays rapidly with physical distance, which is consistent with this interval of PAR1 being recombinationally active in male meiosis. Analysis of a subregion of 9.9 kb in sperm shows, however, that crossovers are not distributed randomly, but instead cluster into an intense recombination hot spot that is very similar in morphology to autosomal hot spots. Thus, PAR1 crossover activity may be influenced by male-specific hot spots that are highly suitable for characterization by sperm DNA analysis.

Base Sequence↗

PubMed1984

Crossover and self-controlled designs in clinical research.

Crossover studies (clinical trials in which each patient receives two or more treatments in sequence) and self-controlled studies (in which each patient serves as his or her own control) can produce results that are statistically and clinically valid with far fewer patients than would otherwise be required. We investigated the use of the crossover design in the 13 crossover studies that appeared in the Journal during 1978 and 1979. We considered the following important features of design and analysis as they applied to these studies: the method by which patients were assigned to initial treatment (only 7 of 13 studies used random assignment); the determination of when to switch treatments (10 of the 13 used a time-dependent rule, and 3 a less appropriate disease-state-dependent rule); blinding of the crossover point (in only 3 of the 13 studies was the crossover point concealed, but in 4 of the remaining 10 concealment was impossible); assessment of the effects of the order of treatments (included in only 1 of the 13 studies); and the use of at least minimally acceptable statistical analysis (11 of the 13 studies had such an analysis). We also report briefly on 28 additional studies of a single treatment each, in which each patient served as his or her own control before or after treatment or both. The scientific issues were much the same as in crossover studies except that self-controlled comparisons of treatments tended to be less precisely designed and conducted and to focus on clinical problems and patient groups that are especially difficult to study.

Chronic Disease↗

PubMed2001

Predicting crossover generation in DNA shuffling.

We introduce a quantitative framework for assessing the generation of crossovers in DNA shuffling experiments. The approach uses free energy calculations and complete sequence information to model the annealing process. Statistics obtained for the annealing events then are combined with a reassembly algorithm to infer crossover allocation in the reassembled sequences. The fraction of reassembled sequences containing zero, one, two, or more crossovers and the probability that a given nucleotide position in a reassembled sequence is the site of a crossover event are estimated. Comparisons of the predictions against experimental data for five example systems demonstrate good agreement despite the fact that no adjustable parameters are used. An in silico case study of a set of 12 subtilases examines the effect of fragmentation length, annealing temperature, sequence identity and number of shuffled sequences on the number, type, and distribution of crossovers. A computational verification of crossover aggregation in regions of near-perfect sequence identity and the presence of synergistic reassembly in family DNA shuffling is obtained.

Algorithms↗

PubMed2006

Testing for crossover of two hazard functions using Gail and Simon's method.

Crossover of two hazard functions is sometimes called qualitative nonproportionality where the hazard ratio could be >1 in some time intervals but <1 in some other intervals. Investigators often wish to know whether a beneficial treatment effect exists over a long period of time (i.e., no crossover). This information is important for the management of safety and efficacy of a new treatment in long-term use. Also, if crossover occurs, the commonly used statistical methods, such as Cox proportional hazards model or linear rank tests, may not be appropriate. Graphical display may be used to visually examine whether there are crossovers in the observed hazard functions. A relevant question is whether the observed crossover of two hazard functions is due to chance variation. In this article, we propose a class of tests for crossover of two hazard functions. The study follow-up period is divided into nonoverlapping time intervals, and the weighted linear rank statistic, including logrank and generalized Wilcoxon statistics, can be calculated from each interval. These statistics are asymptotically independent and have normal distributions. Treating each interval as a "patient subset," qualitative tests of interactions between treatment and patient subsets can naturally apply. For our purpose, we consider the likelihood ratio test proposed by Gail and Simon. Two examples are used to illustrate this approach. The proposed test procedures are also studied through simulations.

Antineoplastic Agents↗

PubMed2002

On statistical power for average bioequivalence testing under replicated crossover designs.

In its recent guidance on bioequivalence, the U.S. Food and Drug Administration (FDA) recommends a two-sequence, four-period (2 x 4) replicated crossover design be used for assessment of population and individual bioequivalence [FDA. Guidance for Industry on Statistical Approaches to Establishing Bioequivalence; Center for Drug Evaluation and Research, Food and Drug Administration: Rockville, MD, 2001]. The recommended replicated crossover design not only allows estimates of both the inter-subject and the intra-subject variabilities and the variability due to subject-by-formulation interaction, but also provides an assessment of average bioequivalence (ABE). In this article, power function for assessment of ABE under a general replicated crossover design (i.e., a 2 x 2m replicated crossover design) based on the traditional analysis of variance model and the mixed effects model as suggested by the FDA are studied. It is found that the power of a 2 x 2m replicated crossover design depends upon the variability due to subject-by-formulation interaction and the number of replicates. Based on the derived power function, formula for sample size calculation for assessment of ABE under a 2 x 2m replicated crossover design is also provided.

Algorithms↗

PubMed2004

Individual differences in response to randomly assigned active individualized homeopathic and placebo treatment in fibromyalgia: implications of a double-blinded optional crossover design.

OBJECTIVE: To assess individual difference characteristics of subgroups of patients with fibromyalgia (FM) patients with respect to the decision to stay in or switch from randomly-assigned verum or placebo treatment during an optional crossover phase of a double-blinded homeopathy study. DESIGN: Double-blinded, randomized, placebo-controlled, optional crossover clinical trial. PARTICIPANTS: Fifty-three (53) community-recruited patients with FM entered the optional crossover phase. INTERVENTION: Two homeopaths jointly selected an individualized homeopathic remedy for all patients. The pharmacy dispensed either verum LM remedy or indistinguishable placebo in accord with randomized assignment for 4 months and the patient's optional crossover decision for an additional 2 months. OUTCOME MEASURES: Patients completed a battery of baseline state/trait questionnaires, including mood, childhood neglect and abuse, and trait absorption. They rated global health (whole person-centered) and tender point pain on physical examination (disease-specific) at baseline, 3 months, and 6 months. RESULTS: Rates of optional crossover from verum to placebo or placebo to verum were comparable (p = 0.6; 31%, and 41%, respectively). The switch subgroups had greater baseline psychologic issues (emotional neglect in placebo-switch; depression and anger in verum-switch). The verum-stay subgroup scored highest on treatment helpfulness and included all six exceptional responders who fell, prior to crossover, into the top terciles for improvement in both global health and pain. Patients staying in their randomly assigned groups, active or placebo (n = 34), scored significantly higher in trait absorption than did those who switched groups (n = 19). CONCLUSION: Individual difference factors may predict better and poorer responders with FM to specific and nonspecific effects of homeopathic and placebo treatment.

Adult↗

PubMed2006

On the equivalence of case-crossover and time series methods in environmental epidemiology.

The case-crossover design was introduced in epidemiology 15 years ago as a method for studying the effects of a risk factor on a health event using only cases. The idea is to compare a case's exposure immediately prior to or during the case-defining event with that same person's exposure at otherwise similar "reference" times. An alternative approach to the analysis of daily exposure and case-only data is time series analysis. Here, log-linear regression models express the expected total number of events on each day as a function of the exposure level and potential confounding variables. In time series analyses of air pollution, smooth functions of time and weather are the main confounders. Time series and case-crossover methods are often viewed as competing methods. In this paper, we show that case-crossover using conditional logistic regression is a special case of time series analysis when there is a common exposure such as in air pollution studies. This equivalence provides computational convenience for case-crossover analyses and a better understanding of time series models. Time series log-linear regression accounts for overdispersion of the Poisson variance, while case-crossover analyses typically do not. This equivalence also permits model checking for case-crossover data using standard log-linear model diagnostics.

Air Pollution↗

PubMed1994

Double crossover in the human Xp/Yp pseudoautosomal region and its bearing on interference.

Most models on crossover and crossover interference have assumed that the intensity of interference depends inversely on the physical distance separating the respective intervals. The possibility, however, also exists that interference depends on genetic rather than on physical distance. As the human pseudoautosomal region (PAR) on Xp/Yp is physically small, yet genetically a hot spot of recombination in male meiosis, studies on the existence of multiple crossover events may be particularly useful in addressing the question of interference. Our results demonstrate for the first time a double crossover during male meiosis in the human PAR on Xp/Yp. The occurrence of a single obligatory recombination event in this region can, therefore, no longer be taken as a dogma. However, double crossover events seem to remain exceptional and, thus, the model originally suggested by Burgoyne remains globally correct. As both recombination events can be localized within a narrow range of physical distance, theories describing interference due to steric hindrance may have to be reconsidered. This finding may, therefore, have general implications for our understanding of the mechanism of positive and negative crossover interference in mammalian genomes and may be interesting especially for linkage mapping where double recombinations in small intervals tend to be considered as genotyping errors.

Base Sequence↗

PubMed2004

The place of the crossover design in infertility trials: a maximum likelihood approach.

BACKGROUND: For some years, there has been a debate as to the place of the crossover trial in assisted reproduction technology (ART). We aimed to investigate whether crossover and parallel designs result in different estimates of treatment effects. METHODS: We carried out computer simulation of cohorts of patients undergoing either intra-uterine insemination (IUI) or IVF under both parallel and crossover designs, under scenarios involving censoring and carryover effects. Results of the simulation were analysed using a maximum likelihood approach. RESULTS: No relevant difference was found between the designs. The crossover design resulted in slightly more pregnancies than the parallel design. Carryover effects may slightly distort the estimates of treatment effects. Crossover and parallel designs will produce essentially the same statistical estimates of treatment effect and percentage of pregnancies. The crossover design is an acceptable design in infertility research provided the data are analysed correctly.

Clinical Trials as Topic↗

PubMed2006

Crossover frequency and synaptonemal complex length: their variability and effects on human male meiosis.

In this study, immunocytogenetics has been used in combination with the subtelomere-specific multiplex-fluorescent in-situ hybridization (stM-FISH) assay to identify 4681 autosomal synaptonemal complexes (SCs) of two fertile men. Comparisons of crossover maps for each individual SC between two men with extremely different meiotic crossover frequencies show that a low crossover frequency results in (i) a higher frequency of XY pairs and of small SCs without MLH1 foci and (ii) lower frequency of crossovers in the proximity of centromeres. In both cases, the bivalents which most frequently lacked MLH1 foci were the XY pair and the SC21. Analysis of SC length showed that SC arms can be longer or shorter than the corresponding mitotic one. Moreover, for a given SC, the variation in length found in one arm was independent of the variation observed in the other one (e.g. SC1p arms are longer than SC1q arms). The results confirmed that reduction in the crossover frequency may increase the risk of achiasmate small bivalents and that interindividual differences in crossover frequency could explain the variability in the frequencies of aneuploidy in human sperm. How MLH1 foci are positioned within the SC is discussed based on detailed MLH1 foci distributions and interfoci distances. Finally, evidence that the variation of the SC arm length may reflect the abundance of open and of compact chromatin fibers in the arm is shown.

Chromosome Mapping↗

PubMed1991

Direct and crossover PCR amplification to facilitate Tn5supF-based sequencing of lambda phage clones.

The 264 bp mini-transposon Tn5supF was constructed to sequence DNAs cloned in phage lambda without extensive shotgun subcloning or primer walking. Unique sequences near each transposon end serve as primer binding sites, and a supF gene is used to select transposition to lambda. We describe here PCR methods that facilitate Tn5supF-based sequencing. In a first pass, insertions are mapped relative to the ends of the cloned fragment using pairs of primers specific for vector DNA next to the cloning site and for a Tn5supF end. Most insertions not mapped in this step are near the center of the cloned fragment or in the vector arms, and are then mapped relative to the two innermost insertions by 'crossover' PCR. This involves amplification from primers on different DNA molecules, and generates hybrid DNA products whose lengths correspond to the distances between the two insertions. We routinely amplified more than 6 kb in direct PCR and 3 kb in crossover PCR; at the limit we amplified up to approximately 10 kb in direct PCR and approximately 6 kb in crossover PCR, but not reproducibly. Crossover PCR products were also obtained with insertions separated by only 200 bp, indicating that no rare sites are needed to switch templates. PCR products were purified by adsorption and then elution from glass slurry, and sequenced directly. Ladders of more than 400 bp were obtained from primer sites on each DNA strand; 2 kb was read from crossover PCR products, and showed that they were amplified with fidelity. In conclusion, direct and crossover PCR methods expedite transposon insertion mapping, and yield templates for accurate sequencing of both DNA strands.

Autoradiography↗

PubMed2005

Analysis of case-crossover designs using longitudinal approaches: a simulation study.

BACKGROUND: Application of case-crossover designs provides an alternative to time-series analysis for analyzing the health-related effects of air pollution. Although some case-crossover studies can control for trend and seasonality by design, to date they have been analyzed as matched case-control studies. Such analyses may exhibit biases and a lower statistical efficiency than traditional time series analyzed with Poisson. METHODS: In this article, case-crossover studies are treated as cohort studies in which each subject is observed for a short period of time before and/or after the event, thus making possible analyzing with Andersen-Gill and generalized linear mixed models. We conducted a simulation study to compare the behavior of these models applied to case-crossover designs with time series analyzed with Poisson and with case-crossover analyzed by conditional logistic regression. To this end, we created a random variable that follows a Poisson distribution of low (2/day) and high mean events (22/day). This variable is a function of an unobserved confounding variable (that introduces trend and seasonality) and data on small particulate matter (PM10) from Barcelona. In addition, scenarios were created to assess the effect on exposure exerted by autocorrelation and the magnitude of the pollutant coefficient. RESULTS: The full semisymmetric design analyzed with generalized linear mixed models yields good coverage and a high statistical power for air-pollution effect magnitudes close to the real values but shows bias for high effect magnitudes. This bias seems to be attributable to autocorrelation in the exposure variable. CONCLUSIONS: Longitudinal approaches applied to case-crossover designs may prove useful for analyzing the acute effects of environmental exposures.

Air Pollutants↗

PubMed2006

Assessing the trade-offs between crossover and parallel group designs in sleep research.

Sleep researchers invariably struggle with decisions regarding the optimal design for their studies. Whether such studies involve treatment for insomnia, obstructive sleep apnea, or any other sleep disorder, questions arise regarding the respective trade-offs between a parallel group and a crossover design. This study analyzed the variance structure of commonly measured polysomnographic variables in an effort to describe the statistical impact of these alternate designs. The study examined the effects of opioids on sleep and employed multiple crossovers between placebo, MS-contin, and methadone using a double-blind, randomized crossover design. Thirty-seven healthy subjects were studied. Four of the subjects were unable to complete the protocol for a variety of reasons, and polysomnogram data was unavailable for one subject. Data from 37 subjects provide the basis for this analysis. Despite dropouts, the crossover study was approximately four times as efficient as the parallel group design in terms of being able to recognize differences in deep sleep across these conditions. Other polysomnographic variables also favored the crossover design to varying extents. Despite the operational complexity of a crossover design, the statistical efficiency of this approach makes it a preferable approach for designing intervention studies in sleep research.

Adult↗